NM_005228.5(EGFR):c.2577del (p.Lys860fs) AND EGFR-related lung cancer

Clinical significance:Pathogenic (Last evaluated: Oct 5, 2021)
Review status:1 star out of maximum of 4 stars
criteria provided, single submitter

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Based on:: 1 submission [Details]
Record status:: current
Accession:: RCV001348004.2

Allele description [Variation Report for NM_005228.5(EGFR):c.2577del (p.Lys860fs)]

NM_005228.5(EGFR):c.2577del (p.Lys860fs)

Gene:

EGFR:epidermal growth factor receptor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7p11.2

Genomic location:

Preferred name:

NM_005228.5(EGFR):c.2577del (p.Lys860fs)

HGVS:

NC_000007.14:g.55191826del
NG_007726.3:g.177795del
NM_001346897.2:c.2442del
NM_001346898.2:c.2577del
NM_001346899.2:c.2442del
NM_001346900.2:c.2418del
NM_001346941.2:c.1776del
NM_005228.5:c.2577delMANE SELECT
NP_001333826.1:p.Lys815fs
NP_001333827.1:p.Lys860fs
NP_001333828.1:p.Lys815fs
NP_001333829.1:p.Lys807fs
NP_001333870.1:p.Lys593fs
NP_005219.2:p.Lys860fs
LRG_304:g.177795del
NC_000007.13:g.55259518del
NC_000007.13:g.55259519del

Protein change:

K593fs

Links:

dbSNP: rs1787409872

NCBI 1000 Genomes Browser:

rs1787409872

Molecular consequence:

NM_001346897.2:c.2442del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001346898.2:c.2577del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001346899.2:c.2442del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001346900.2:c.2418del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001346941.2:c.1776del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005228.5:c.2577del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: EGFR-related lung cancer (EGFR)
Identifiers:: MedGen: CN130014

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001542289	Invitae	criteria provided, single submitter Invitae Variant Classification Sherloc (09022015)	Pathogenic (Oct 5, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 7630400, 28726809, 29899996, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001542289

Invitae

criteria provided, single submitter

Invitae Variant Classification Sherloc (09022015)

Pathogenic
(Oct 5, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

Help

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Epithelial immaturity and multiorgan failure in mice lacking epidermal growth factor receptor.

Miettinen PJ, Berger JE, Meneses J, Phung Y, Pedersen RA, Werb Z, Derynck R.

Nature. 1995 Jul 27;376(6538):337-41.

PubMed [citation]

PMID:: 7630400

Genomic diagnostics within a medically underserved population: efficacy and implications.

Strauss KA, Gonzaga-Jauregui C, Brigatti KW, Williams KB, King AK, Van Hout C, Robinson DL, Young M, Praveen K, Heaps AD, Kuebler M, Baras A, Reid JG, Overton JD, Dewey FE, Jinks RN, Finnegan I, Mellis SJ, Shuldiner AR, Puffenberger EG.

Genet Med. 2018 Jan;20(1):31-41. doi: 10.1038/gim.2017.76. Epub 2017 Jul 20.

PubMed [citation]

PMID:: 28726809

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001542289.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Lys860Asnfs*43) in the EGFR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EGFR are known to be pathogenic (PMID: 7630400, 28726809, 29899996). This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with EGFR-related conditions. ClinVar contains an entry for this variant (Variation ID: 1043841). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 24, 2022

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