NM_005228.5(EGFR):c.2369C>T (p.Thr790Met)
Reviewed by expert panel. Learn more about how ClinVar calculates review status.
The classification is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
The classification is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
criteria provided, single submitter. Learn more about how ClinVar calculates review status.
The aggregate somatic clinical impact for this variant for one or more tumor types, using the AMP/ASCO/CAP terminology. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
criteria provided, single submitter. Learn more about how ClinVar calculates review status.
The aggregate oncogenicity classification for this variant for one or more tumor types, using the ClinGen/CGC/VICC terminology. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Variant Details
- Identifiers
-
NM_005228.5(EGFR):c.2369C>T (p.Thr790Met)
Variation ID: 16613 Accession: VCV000016613.46
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p11.2 7: 55181378 (GRCh38) [ NCBI UCSC ] 7: 55249071 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jan 31, 2015 Jul 6, 2026 Mar 24, 2021 Somatic - Clinical impact Apr 26, 2026 Apr 25, 2026 Apr 24, 2026 Somatic - Oncogenicity Aug 11, 2024 Mar 11, 2025 Mar 4, 2025 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_005228.5:c.2369C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_005219.2:p.Thr790Met missense NM_001346897.2:c.2234C>T NP_001333826.1:p.Thr745Met missense NM_001346898.2:c.2369C>T NP_001333827.1:p.Thr790Met missense NM_001346899.2:c.2234C>T NP_001333828.1:p.Thr745Met missense NM_001346900.2:c.2210C>T NP_001333829.1:p.Thr737Met missense NM_001346941.2:c.1568C>T NP_001333870.1:p.Thr523Met missense NM_005228.4:c.[2369C>T] NR_047551.1:n.1193G>A non-coding transcript variant NC_000007.14:g.55181378C>T NC_000007.13:g.55249071C>T NG_007726.3:g.167347C>T LRG_304:g.167347C>T LRG_304t1:c.2369C>T P00533:p.Thr790Met - Protein change
- T790M, T745M, T523M, T737M
- Other names
- -
- Canonical SPDI
- NC_000007.14:55181377:C:T
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00005
The Genome Aggregation Database (gnomAD) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00004
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| EGFR | No evidence available | No evidence available |
GRCh38 GRCh37 |
3711 | 4176 | |
| EGFR-AS1 | - | - | - | GRCh38 | - | 271 |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| drug response (2) |
no assertion criteria provided
|
Oct 30, 2020 | RCV000154232.13 | |
| Likely pathogenic (1) |
no assertion criteria provided
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Nov 11, 2014 | RCV000154233.17 | |
| drug response (1) |
reviewed by expert panel
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Mar 24, 2021 | RCV000211319.14 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Jan 26, 2026 | RCV000557450.20 | |
| Likely pathogenic (1) |
criteria provided, single submitter
|
Aug 22, 2025 | RCV001015308.16 | |
| drug response (1) |
reviewed by expert panel
|
Mar 24, 2021 | RCV001787805.13 | |
| Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 31, 2024 | RCV001588815.12 | |
| Pathogenic (2) |
criteria provided, single submitter
|
- | RCV001823098.18 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Dec 7, 2023 | RCV003466864.2 | |
| Likely pathogenic (1) |
no assertion criteria provided
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- | RCV003996105.1 | |
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EGFR-related disorder
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Likely pathogenic (1) |
no assertion criteria provided
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Jun 11, 2024 | RCV004752710.1 |
| click to load more conditions click to collapse | ||||
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Collapse all rows
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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|---|---|---|---|---|---|
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drug response
Drug-variant association: Efficacy
(Mar 24, 2021)
C
Contributing to aggregate classification
|
reviewed by expert panel
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erlotinib response - Efficacy
Drug used for
Adenocarcinoma
, Carcinoma, Non-Small-Cell Lung
, Drug Resistance
, and Lung Neoplasms
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ClinPGx
Accession: SCV000268172.4
First in ClinVar: May 22, 2016 Last updated: Dec 12, 2021
Comment:
Drug is not necessarily used to treat response condition
|
Comment:
show
PharmGKB Level of Evidence 2B: Variants in Level 2B clinical annotations are not in PharmGKB’s Tier 1 VIPs. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2B clinical annotations must be supported by at least two independent publications. (less)
Observation: 1
Collection method: curation
Allele origin: germline
Affected status: yes
Observation 1
Collection method: curation
Allele origin: germline
Affected status: yes
|
|
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drug response
Drug-variant association: Efficacy
(Mar 24, 2021)
C
Contributing to aggregate classification
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reviewed by expert panel
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gefitinib response - Efficacy
Drug used for
Carcinoma, Non-Small-Cell Lung
, and Drug Resistance
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ClinPGx
Accession: SCV002031219.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021
Comment:
Drug is not necessarily used to treat response condition
|
Comment:
show
PharmGKB Level of Evidence 2B: Variants in Level 2B clinical annotations are not in PharmGKB’s Tier 1 VIPs. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2B clinical annotations must be supported by at least two independent publications. (less)
Observation: 1
Collection method: curation
Allele origin: germline
Affected status: yes
Observation 1
Collection method: curation
Allele origin: germline
Affected status: yes
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Pathogenic
(-)
N
Not contributing to aggregate classification
|
criteria provided, single submitter
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Lung cancer |
Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV002073070.1
First in ClinVar: Feb 05, 2022 Last updated: Feb 05, 2022 |
Comment:
show
The missense variant p.T790M in EGFR (NM_005228.5) has been reported in multiple patients with adenocarcinoma of lung. In majority of the cases the mutation has been detected by somatic testing. Germline mutation T790M has been reported in a subset of patients both with and without disease implying incomplete penetrance (Helena Yu A et al, 2014; Gazdar A et al, 2014; Oxnard GR et al, 2012; Tibaldi C et al, 2011). The variant has been classified by the expert review panel in Clin Var as Pathogenic with respect to drug response. It is present in 10 alleles in heterozygote state (0.003%) in the gnomAD database. There is a moderate physicochemical difference between threonine and methionine. The p.T790M missense variant is predicted to be damaging by both SIFT and PolyPhen2. The nucleotide c.2369 in EGFR is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Clinical Features:
Prostate cancer (present) , Neoplasm of lung (present) , Paralytic lagophthalmos (present)
Comment on clinical features:
62 year male presented with family history of prostate, lung and colon cancer was referred for genetic evaluation.
|
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likely pathogenic
(Dec 31, 2024)
N
Not contributing to aggregate classification
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criteria provided, single submitter
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not provided |
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV007111203.1
First in ClinVar: Dec 07, 2025 Last updated: Dec 07, 2025 |
Comment:
show
The EGFR c.2369C>T (p.Thr790Met) variant has been reported in the published literature in individuals with lung cancer (PMID: 33858029 (2021), 34012789 (2021), 30610926 (2019), 28947568 (2017), 28843361 (2017), 26700910 (2016), 23540867 (2013), 22588155 (2012), 22588155 (2012), 21252721 (2011)), breast cancer (PMID: 37265791 (2023)), and sarcoma (PMID: 35573754 (2022)). As a somatic variant, it confers drug resistance to tyrosine kinase inhibitors (PMID: 36849516 (2023), 24478319 (2014)). Additionally, as a germline variant, it segregates with disease in multiple families and is associated with an increased risk of lung cancer (PMID: 37579253 (2023), 24736066 (2014), 20068085 (2010), 16258541 (2005)). Functional studies indicate that this variant promotes tumor development and drug resistance (PMID: 39066480 (2024), 18227510 (2008), 17726540 (2007), 17510392 (2007), 15737014 (2005), 15728811 (2005)). The frequency of this variant in the general population (Genome Aggregation Database, http://gnomad.broadinstitute.org) is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as likely pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
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Likely pathogenic
(Sep 08, 2020)
N
Not contributing to aggregate classification
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criteria provided, single submitter
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not provided |
GeneDx
Accession: SCV001825948.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021 |
Comment:
show
In summary, in vivo experiments demonstrated that T790M drives lung adenocarcinomas and is required for tumor maintenance (Regales et al., 2007); In vitro experiments demonstrated that T790M activated EGFR signaling pathway and provided a growth advantage for cancer cells (Viskis et al., 2007); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 33504652, 29625052, 30610926, 30225213, 28989039, 23817662, 24736066, 24736080, 24453288, 11423618, 22426079, 26700910, 28125075, 28843361, 28982744, 28947568, 23540867, 19096324, 16258541, 22588155, 20068085, 24478319, 17726540, 18227510, 17510392, 15728811, 18632637, 24053674, 15737014, 27251290, 15272417, 20033049, 21252721, 26799287, 27734950) (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
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Pathogenic
(Dec 07, 2023)
N
Not contributing to aggregate classification
|
criteria provided, single submitter
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Inflammatory skin and bowel disease, neonatal, 2 |
Baylor Genetics
Accession: SCV004194584.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
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Likely pathogenic
(Aug 22, 2025)
N
Not contributing to aggregate classification
|
criteria provided, single submitter
|
Hereditary cancer-predisposing syndrome |
Ambry Genetics
Accession: SCV001176128.7
First in ClinVar: Mar 16, 2020 Last updated: Oct 05, 2025 |
Comment:
show
The p.T790M variant (also known as c.2369C>T), located in coding exon 20 of the EGFR gene, results from a C to T substitution at nucleotide position 2369. The threonine at codon 790 is replaced by methionine, an amino acid with similar properties. This alteration is a well known somatic alteration that is acquired and confers resistance to tyrosine kinase inhibitors which are agents used to treat lung cancer (Pao W et al. PLoS Med., 2005 Mar;2:e73). However, it has also been identified in the germline of many individuals with a personal and/or family history of lung cancer and segregates with lung cancer in some of these families, including in people who are considered never-smokers (Bell DW et al. Nat. Genet. 2005 Dec;37:1315-6; Prudkin L et al. J Thorac Oncol, 2009 Jan;4:139-41; Girard N et al. Clin. Cancer Res., 2010 Jan;16:755-63; Tibaldi C et al. J Thorac Oncol. 2011 Feb;6:395-6; Oxnard GR et al. J Thorac Oncol, 2012 Jun;7:1049-52; Thomas A et al. Clin Lung Cancer, 2013 Jul;14:452-6; Gazdar A et al. J Thorac Oncol. 2014 Apr;9:456-63; Yu HA et al. J Thorac Oncol. 2014 Apr;9:554-8; Lou Y et al. Clin Lung Cancer, 2016 Mar;17:e5-11; Hu Y et al. Clin. Cancer Res., 2017 Dec;23:7351-7359; Huang KL et al. Cell 2018 04;173(2):355-370.e14; Lu S et al. J Thorac Oncol. 2019 04;14:732-736; Reckamp KL et al. Cancer, 2021 Aug;127:2801-2806). Functional studies have shown that this alteration precludes binding of some TKIs, but that it also increases the binding affinity of EGFR for ATP which would lead to increased activation of the protein and increased cell growth (Pao W et al. PLoS Med., 2005 Mar;2:e73; Kobayashi S et al. N. Engl. J. Med., 2005 Feb;352:786-92; Regales L et al. PLoS ONE, 2007 Aug;2:e810; Yun CH et al. Proc. Natl. Acad. Sci. U.S.A., 2008 Feb;105:2070-5; Vikis H et al. Cancer Res., 2007 May;67:4665-70). Mice expressing an inducible transgene carrying this alteration develop lung adenocarcinomas, and this alteration is required for them to maintain their tumors (Regales L et al. PLoS ONE, 2007 Aug;2:e810). This alteration has a preliminary risk estimate of 31% in never smokers (Gazdar A et al. J Thorac Oncol, 2014 Apr;9:456-63). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is likely pathogenic for EGFR-related lung cancer; however, the association of this alteration with EGFR-related neonatal inflammatory skin and bowel disease is unknown. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
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Pathogenic
(Jan 26, 2026)
N
Not contributing to aggregate classification
|
criteria provided, single submitter
|
EGFR-related lung cancer |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000658980.11
First in ClinVar: Dec 26, 2017 Last updated: Mar 07, 2026 |
Comment:
show
This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 790 of the EGFR protein (p.Thr790Met). This variant is present in population databases (rs121434569, gnomAD 0.02%). This missense change has been observed in individual(s) with lung cancer (PMID: 16258541, 21252721, 23540867, 24736066, 24736080, 26700910, 37579253). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 16613). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt EGFR protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects EGFR function (PMID: 15728811, 15737014, 17510392, 17726540, 18227510). For these reasons, this variant has been classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
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drug response
(Nov 11, 2014)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Tyrosine kinase inhibitor response |
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000203887.1
First in ClinVar: Jan 31, 2015 Last updated: Jan 31, 2015 |
Comment:
show
The Thr790Met variant in EGFR has been identified as a somatic change in individuals with non-small cell lung cancer (NSCLC) that have an acquired resistance to EGFR-tyrosine kinase inhibitors (TKIs), often in combination with other EGFR kinase domain mutations (Pao 2005). This variant has been found to arise in 60% of patients with acquired resistance to TKIs. In summary, the Thr790Met variant meets our criteria to be classified as resistant (http://pcpgm.partners.org/LMM). (less)
Observation: 1
Collection method: clinical testing
Allele origin: somatic
Affected status: not provided
Observation 1
Collection method: clinical testing
Allele origin: somatic
Affected status: not provided
Number of individuals with the variant: 85
|
|
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Likely pathogenic
(Nov 11, 2014)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Non-Small Cell Lung Cancer |
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000203888.1
First in ClinVar: Jan 31, 2015 Last updated: Jan 31, 2015 |
Comment:
show
The p.Thr790Met variant in EGFR has been identified as a somatic change in individuals with non-small cell lung cancer (NSCLC) that have an acquired resistance to EGFR-tyrosine kinase inhibitors (TKIs), often in combination with other EGFR kinase domain mutations (Pao 2005). In addition, this variant has been identified as a germline mutation in at least 14 unrelated individuals with NSCLC (including never smokers; Bell 2005, Prudkin 2009, Girard 2010, Tibaldi 2011, Oxnard 2012, Thomas 2013, Gazdar 2014, Yu 2014) and segregated with lung cancer and pulmonary disease in at least 4 affected individuals from 3 families (Bell 2005, Gazdar 2012, Yu 2014). This variant was absent from large population studies. While the literature reports strongly suggest that the p.Thr790Met variant can predispose to lung cancer, the penetrance of a germline p.Thr790Met variant has not been established and the functional impact of this variant in the germline is not well understood. In summary, this variant is likely to be pathogenic, though additional studies are required to fully establish its clinical significance. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Number of individuals with the variant: 85
|
|
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Likely pathogenic
(Jun 11, 2024)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
EGFR-related condition
|
PreventionGenetics, part of Exact Sciences
Accession: SCV005362384.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
show
The EGFR c.2369C>T variant is predicted to result in the amino acid substitution p.Thr790Met. This variant has been identified in multiple individuals with personal and/or family history of lung cancer, many of whom were never smokers (see for example, Bell et al. 2005. PubMed ID: 16258541; Gazdar et al 2014. PubMed ID: 24736066). In addition, this variant has been consistently demonstrated to affect tyrosine kinase inhibition in individuals with non-small cell lung cancers (see for example, Figure 1, Bell et al. 2005. PubMed ID: 16258541; Table 4, Chen et al. 2009. PubMed ID: 19381876; Table 1, Sequist et al. 2011. PubMed ID: 21430269). This variant is reported in 0.016% of alleles in individuals of African descent in gnomAD. This variant has been classified as a drug response variant by an expert panel and is consistently classified as pathogenic and likely pathogenic by other institutions in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/16613/). This variant is interpreted as likely pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
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Pathogenic
(Dec 24, 2009)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
NONSMALL CELL LUNG CANCER, RESISTANCE TO TYROSINE KINASE INHIBITOR IN, SOMATIC
|
OMIM
Accession: SCV000038367.8
First in ClinVar: Apr 04, 2013 Last updated: Jul 06, 2026 |
Observation: 1
Collection method: literature only
Allele origin: somatic
Affected status: not provided
Observation 1
Collection method: literature only
Allele origin: somatic
Affected status: not provided
Comment on evidence:
In a tumor with the 2240del18 mutation in the EGFR gene (131550.0001) from a patient with nonsmall cell lung cancer (211980) who showed responsiveness to … (more)
In a tumor with the 2240del18 mutation in the EGFR gene (131550.0001) from a patient with nonsmall cell lung cancer (211980) who showed responsiveness to gefitinib with complete remission over a 2-year period, Kobayashi et al. (2005) identified the development of a second mutation in EGFR, thr790 to met (T790M), responsible for secondary resistance to gefitinib. Kobayashi et al. (2005) noted that one of the most common imatinib resistance mutations in ABL1/BCR in leukemia replaces threonine at position 315 (the amino acid structurally corresponding to T790 of EGFR) with isoleucine in the ABL tyrosine kinase domain (thr315 to ile; 189980.0001). The T315I substitution leads to a structural change very similar to that observed with T790M (Gorre et al., 2001). In 2 women with nonsmall cell lung cancer, Toyooka et al. (2005) identified 2 EGFR mutations, T790M and L858R (131550.0002), in resected tumor specimens taken before treatment with chemotherapy or radiation. Both patients later had recurrent disease and eventually died, suggesting that tumors with both these mutations are very aggressive. One patient was treated with gefitinib and had progression. Approximately 10% on of nonsmall cell lung cancers respond markedly to treatment with tyrosine kinase inhibitors that target EGFR. Responsive tumors are characteristically adenocarcinomas, often with bronchoalveolar (BAC) differentiation, and they are most common in nonsmokers, women, and Asians. Molecular analyses identified specific mutations in the kinase domain of EGFR in approximately 80% of responsive cases, e.g., an 18-bp deletion (131550.0001) and a missense mutation, L858R (131550.0002). These characteristic missense mutations and in-frame deletions affect residues of the ATP binding pocket, selectively enhancing ligand-dependent activation of the AKT/STAT survival pathways by the receptor. The T790M mutation was reported in cases of nonsmall cell lung cancers that recurred after initial response to tyrosine kinase inhibitors. Bell et al. (2005) studied a family of European descent in which multiple members developed the BAC subtype of nonsmall cell lung cancer. Six persons in 3 generations were affected. The cancer was found to be associated with germline transmission of the T790M mutation, suggesting that this mutation confers a growth advantage even in the absence of selective pressure of a tyrosine kinase inhibitor. Four of 6 tumors analyzed showed a secondary somatic activating EGFR mutation, arising in cis with the germline EGFR mutation T790M. These observations implicated altered EGFR signaling in genetic susceptibility to lung cancer. Yun et al. (2008) noted that thr790 is located at the entrance to a hydrophobic pocket in the back of the ATP binding cleft of EGFR. Substitution of thr790 with a bulky methionine has been postulated to cause resistance to reversible tyrosine kinase inhibitors through steric interference. However, Yun et al. (2008) used crystal structure analysis to show that certain irreversible inhibitors could still bind to the T790M-mutant EGFR, which is inconsistent with steric interference as a mechanism of drug resistance. Kinetic studies indicated that the L858R/T790M mutant receptor had increased ATP affinity compared to the L858R mutant alone, restoring ATP affinity close to that of wildtype. The T790M mutant alone and with L858R significantly increased kinase activity compared to wildtype. Yun et al. (2008) concluded that the T790M mutation will reduce the potency of any ATP-competitive kinase inhibitor, and that the primary mechanism of drug resistance conferred by T790M is increased ATP affinity. Zhou et al. (2009) identified a covalent pyrimidine EGFR inhibitor by screening an irreversible kinase inhibitor library specifically against EGFR T790M. These agents are 30- to 100-fold more potent against EGFR T790M, and up to 100-fold less potent against wildtype EGFR, than quinazoline-based EGFR inhibitors in vitro. They were also affected in murine models of lung cancer driven by EGFR T790M. (less)
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drug response
(Oct 30, 2020)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Tyrosine kinase inhibitor response
Drug used for
Non-small cell lung cancer
|
Institute of Medical Sciences, Banaras Hindu University
Accession: SCV001571408.1
First in ClinVar: Apr 18, 2021 Last updated: Apr 18, 2021 |
Observation: 1
Collection method: research
Allele origin: somatic
Affected status: yes
Observation 1
Collection method: research
Allele origin: somatic
Affected status: yes
|
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Likely pathogenic
(-)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Adenocarcinoma of lung |
Key Laboratory of Carcinogenesis and Cancer Invasion, Central South University
Accession: SCV004042717.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024 |
Observation: 1
Collection method: clinical testing
Allele origin: somatic
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: somatic
Affected status: yes
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Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| CRISPR-mediated ablation of TP53 and EGFR mutations enhances gefitinib sensitivity and anti-tumor efficacy in lung cancer. | Yoon AR | Molecular therapy : the journal of the American Society of Gene Therapy | 2024 | PMID: 39066480 |
| Germline EGFR Mutations and Familial Lung Cancer. | Oxnard GR | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2023 | PMID: 37579253 |
| Case report: Neuroendocrine breast carcinoma with a germline EGFR T790M mutation. | Sagan OA | Frontiers in oncology | 2023 | PMID: 37265791 |
| Analysis of acquired resistance mechanisms to osimertinib in patients with EGFR-mutated advanced non-small cell lung cancer from the AURA3 trial. | Chmielecki J | Nature communications | 2023 | PMID: 36849516 |
| A Case of Isolated Myeloid Sarcoma Associated With Germline EGFR T790M Variant: The Importance of Recognizing Potential Germline Variants on Somatic Tumor Sequencing Panels. | Walker M | Journal of hematology | 2022 | PMID: 35573754 |
| Presentation of EGFR mutations in 162 family probands with multiple primary lung cancer. | Li C | Translational lung cancer research | 2021 | PMID: 34012789 |
| Germline mutations and age at onset of lung adenocarcinoma. | Reckamp KL | Cancer | 2021 | PMID: 33858029 |
| EGFR and ERBB2 Germline Mutations in Chinese Lung Cancer Patients and Their Roles in Genetic Susceptibility to Cancer. | Lu S | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2019 | PMID: 30610926 |
| Discrimination of Germline EGFR T790M Mutations in Plasma Cell-Free DNA Allows Study of Prevalence Across 31,414 Cancer Patients. | Hu Y | Clinical cancer research : an official journal of the American Association for Cancer Research | 2017 | PMID: 28947568 |
| Germline Mutations in DNA Repair Genes in Lung Adenocarcinoma. | Parry EM | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2017 | PMID: 28843361 |
| Germline Mutation of T790M and Dual/Multiple EGFR Mutations in Patients With Lung Adenocarcinoma. | Lou Y | Clinical lung cancer | 2016 | PMID: 26700910 |
| Germline EGFR T790M mutation found in multiple members of a familial cohort. | Yu HA | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2014 | PMID: 24736080 |
| Hereditary lung cancer syndrome targets never smokers with germline EGFR gene T790M mutations. | Gazdar A | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2014 | PMID: 24736066 |
| Poor response to erlotinib in patients with tumors containing baseline EGFR T790M mutations found by routine clinical molecular testing. | Yu HA | Annals of oncology : official journal of the European Society for Medical Oncology | 2014 | PMID: 24478319 |
| A patient with metastatic lung adenocarcinoma harboring concurrent EGFR L858R, EGFR germline T790M, and PIK3CA mutations: the challenge of interpreting results of comprehensive mutational testing in lung cancer. | Lammers PE | Journal of the National Comprehensive Cancer Network : JNCCN | 2014 | PMID: 24453288 |
| The quest to overcome resistance to EGFR-targeted therapies in cancer. | Chong CR | Nature medicine | 2013 | PMID: 24202392 |
| Concurrent molecular alterations in tumors with germ line epidermal growth factor receptor T790M mutations. | Thomas A | Clinical lung cancer | 2013 | PMID: 23540867 |
| Screening for germline EGFR T790M mutations through lung cancer genotyping. | Oxnard GR | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2012 | PMID: 22588155 |
| Pretreatment epidermal growth factor receptor (EGFR) T790M mutation predicts shorter EGFR tyrosine kinase inhibitor response duration in patients with non-small-cell lung cancer. | Su KY | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2012 | PMID: 22215752 |
| A noninvasive system for monitoring resistance to epidermal growth factor receptor tyrosine kinase inhibitors with plasma DNA. | Nakamura T | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2011 | PMID: 21921847 |
| Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. | Sequist LV | Science translational medicine | 2011 | PMID: 21430269 |
| Inherited germline T790M mutation and somatic epidermal growth factor receptor mutations in non-small cell lung cancer patients. | Tibaldi C | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2011 | PMID: 21252721 |
| Rebiopsy of lung cancer patients with acquired resistance to EGFR inhibitors and enhanced detection of the T790M mutation using a locked nucleic acid-based assay. | Arcila ME | Clinical cancer research : an official journal of the American Association for Cancer Research | 2011 | PMID: 21248300 |
| Pretreatment EGFR T790M mutation and BRCA1 mRNA expression in erlotinib-treated advanced non-small-cell lung cancer patients with EGFR mutations. | Rosell R | Clinical cancer research : an official journal of the American Association for Cancer Research | 2011 | PMID: 21233402 |
| Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC. | Turke AB | Cancer cell | 2010 | PMID: 20129249 |
| Analysis of genetic variants in never-smokers with lung cancer facilitated by an Internet-based blood collection protocol: a preliminary report. | Girard N | Clinical cancer research : an official journal of the American Association for Cancer Research | 2010 | PMID: 20068085 |
| Acquired resistance to gefitinib: the contribution of mechanisms other than the T790M, MET, and HGF status. | Onitsuka T | Lung cancer (Amsterdam, Netherlands) | 2010 | PMID: 19589612 |
| Novel mutant-selective EGFR kinase inhibitors against EGFR T790M. | Zhou W | Nature | 2009 | PMID: 20033049 |
| Clinicopathologic and molecular features of epidermal growth factor receptor T790M mutation and c-MET amplification in tyrosine kinase inhibitor-resistant Chinese non-small cell lung cancer. | Chen HJ | Pathology oncology research : POR | 2009 | PMID: 19381876 |
| Germ-line and somatic presentations of the EGFR T790M mutation in lung cancer. | Prudkin L | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 2009 | PMID: 19096324 |
| Prospective phase II study of gefitinib in non-small cell lung cancer with epidermal growth factor receptor gene mutations. | Sugio K | Lung cancer (Amsterdam, Netherlands) | 2009 | PMID: 18992959 |
| Effects of erlotinib in EGFR mutated non-small cell lung cancers with resistance to gefitinib. | Costa DB | Clinical cancer research : an official journal of the American Association for Cancer Research | 2008 | PMID: 18981003 |
| Detection of mutations in EGFR in circulating lung-cancer cells. | Maheswaran S | The New England journal of medicine | 2008 | PMID: 18596266 |
| The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. | Yun CH | Proceedings of the National Academy of Sciences of the United States of America | 2008 | PMID: 18227510 |
| MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib. | Bean J | Proceedings of the National Academy of Sciences of the United States of America | 2007 | PMID: 18093943 |
| Development of new mouse lung tumor models expressing EGFR T790M mutants associated with clinical resistance to kinase inhibitors. | Regales L | PloS one | 2007 | PMID: 17726540 |
| EGFR-T790M is a rare lung cancer susceptibility allele with enhanced kinase activity. | Vikis H | Cancer research | 2007 | PMID: 17510392 |
| Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors. | Balak MN | Clinical cancer research : an official journal of the American Association for Cancer Research | 2006 | PMID: 17085664 |
| Analysis of epidermal growth factor receptor gene mutation in patients with non-small cell lung cancer and acquired resistance to gefitinib. | Kosaka T | Clinical cancer research : an official journal of the American Association for Cancer Research | 2006 | PMID: 17020982 |
| Presence of epidermal growth factor receptor gene T790M mutation as a minor clone in non-small cell lung cancer. | Inukai M | Cancer research | 2006 | PMID: 16912157 |
| Inherited susceptibility to lung cancer may be associated with the T790M drug resistance mutation in EGFR. | Bell DW | Nature genetics | 2005 | PMID: 16258541 |
| EGFR mutation and response of lung cancer to gefitinib. | Toyooka S | The New England journal of medicine | 2005 | PMID: 15901872 |
| Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. | Pao W | PLoS medicine | 2005 | PMID: 15737014 |
| EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. | Kobayashi S | The New England journal of medicine | 2005 | PMID: 15728811 |
| A major lung cancer susceptibility locus maps to chromosome 6q23-25. | Bailey-Wilson JE | American journal of human genetics | 2004 | PMID: 15272417 |
| Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. | Gorre ME | Science (New York, N.Y.) | 2001 | PMID: 11423618 |
| https://www.pharmgkb.org/clinicalAnnotation/1451250540 | - | - | - | - |
| https://www.pharmgkb.org/clinicalAnnotation/981475450 | - | - | - | - |
| https://www.pharmgkb.org/variant/PA166157528 | - | - | - | - |
| click to load more citations click to collapse | ||||
Conditions - Somatic
| Tumor type
Help
The tumor type for this variant-condition (RCV) record in ClinVar. |
Clinical impact (# of submissions)
Help
The aggregate somatic clinical impact for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to the aggregate somatic clinical impact is shown in parentheses. The corresponding review status for the RCV record is indicated by stars. Read our rules for calculating the review status. |
Oncogenicity
Help
The aggregate oncogenicity classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to the aggregate oncogenicity classification is shown in parentheses. The corresponding review status for the RCV record is indicated by stars. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the tumor type. |
Variation/condition record
Help
The most recent date that a submitter evaluated this variant for the tumor type. |
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Tier I (Strong)
- therapeutic
- sensitivity/response
(1)
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Apr 24, 2026 | RCV000154233.17 | ||
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Oncogenic
criteria provided, single submitter
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Mar 4, 2025 | RCV004668735.2 |
Submissions - Somatic
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Clinical impact
Help
The submitted somatic clinical impact for each SCV record. (Last evaluated) |
Review Status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Tumor type
Help
The tumor type for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Help
This column includes more information supporting the somatic clinical impact, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Tier I (Strong)
- Therapeutic
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sensitivity/response - Osimertinib (Apr 24, 2026)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Lung Non-small Cell Carcinoma |
CIViC Knowledgebase, Washington University School of Medicine
Accession: SCV007579162.1
First In ClinVar: Apr 25, 2026 Last updated: Apr 25, 2026 |
Comment:
show
The EGFR T790M mutation occurs in approximately 50-60% of EGFR mutated non small cell lung cancer (NSCLC) patients treated with first or second-generation EGFR tyrosine kinase inhibitors (TKIs). The third-generation EGFR TKI osimertinib has been shown to inhibit proliferation signaling and growth in cell line and xenograft models (civic.EID:963) and human cell lines (civic.EID:967) with EGFR T790M. Case study reports indicate benefit from osimertinib for NSCLC patients with primary sensitizing EGFR mutations who progressed on first line TKI treatment with the emergence of T790M (civic.EID:12946). Osimertinib was given accelerated approval for treatment of T790M positive NSCLC patients who had progressed on previous TKI therapy based on results from a Phase I study showing a 59% objective response rate to osimertinib in these patients (civic.EID:965), and then granted regular approval after the confirmatory phase 3 trial (AURA3) further indicated benefit with a 71 percent overall response rate in T790M patients who had progressed on TKI therapy versus 31 percent response rate with chemotherapy (civic.EID:1867). (less)
Observation: 1
Collection method: curation
Allele origin: somatic
Affected status: unknown
Observation 1
Collection method: curation
Allele origin: somatic
Affected status: unknown
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Oncogenicity
Help
The submitted oncogenicity classification for each SCV record. (Last evaluated) |
Review Status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Tumor type
Help
The tumor type for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Help
This column includes more information supporting the somatic clinical impact, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Oncogenic
(Mar 04, 2025)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Neoplasm |
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV005094135.2
First In ClinVar: Aug 11, 2024 Last updated: Mar 11, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: somatic
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: somatic
Affected status: yes
|
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Citations for somatic classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| An unbiased in vitro screen for activating epidermal growth factor receptor mutations. | Chakroborty D | The Journal of biological chemistry | 2019 | PMID: 30952700 |
| Structural and mechanistic underpinnings of the differential drug sensitivity of EGFR mutations in non-small cell lung cancer. | Eck MJ | Biochimica et biophysica acta | 2010 | PMID: 20026433 |
| The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. | Yun CH | Proceedings of the National Academy of Sciences of the United States of America | 2008 | PMID: 18227510 |
| Oncogenic activity of epidermal growth factor receptor kinase mutant alleles is enhanced by the T790M drug resistance mutation. | Godin-Heymann N | Cancer research | 2007 | PMID: 17671201 |
| https://civicdb.org/links/evidence/1592 | - | - | - | - |
| https://civicdb.org/links/evidence/1867 | - | - | - | - |
| https://civicdb.org/links/evidence/963 | - | - | - | - |
| https://civicdb.org/links/evidence/965 | - | - | - | - |
| https://civicdb.org/links/evidence/966 | - | - | - | - |
| https://civicdb.org/links/evidence/967 | - | - | - | - |
| https://pubmed.ncbi.nlm.nih.gov/24893891 | - | - | - | - |
| https://pubmed.ncbi.nlm.nih.gov/25923549 | - | - | - | - |
| https://pubmed.ncbi.nlm.nih.gov/26515464 | - | - | - | - |
| https://pubmed.ncbi.nlm.nih.gov/26720284 | - | - | - | - |
| https://pubmed.ncbi.nlm.nih.gov/26729184 | - | - | - | - |
| https://pubmed.ncbi.nlm.nih.gov/27959700 | - | - | - | - |
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Text-mined citations for rs121434569 ...
HelpRecord last updated Jul 06, 2026
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
