ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.4952A>G (p.Asn1651Ser)
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000548.5(TSC2):c.4952A>G (p.Asn1651Ser)
Variation ID: 49335 Accession: VCV000049335.16
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16p13.3 16: 2086834 (GRCh38) [ NCBI UCSC ] 16: 2136835 (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 Sep 16, 2013 Feb 25, 2025 Apr 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000548.5:c.4952A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Asn1651Ser missense NM_000548.4:c.4952A>G NM_001077183.3:c.4751A>G NP_001070651.1:p.Asn1584Ser missense NM_001114382.3:c.4883A>G NP_001107854.1:p.Asn1628Ser missense NM_001318827.2:c.4643A>G NP_001305756.1:p.Asn1548Ser missense NM_001318829.2:c.4607A>G NP_001305758.1:p.Asn1536Ser missense NM_001318831.2:c.4220A>G NP_001305760.1:p.Asn1407Ser missense NM_001318832.2:c.4784A>G NP_001305761.1:p.Asn1595Ser missense NM_001363528.2:c.4754A>G NP_001350457.1:p.Asn1585Ser missense NM_001370404.1:c.4820A>G NP_001357333.1:p.Asn1607Ser missense NM_001370405.1:c.4823A>G NP_001357334.1:p.Asn1608Ser missense NM_021055.3:c.4823A>G NP_066399.2:p.Asn1608Ser missense NC_000016.10:g.2086834A>G NC_000016.9:g.2136835A>G NG_005895.1:g.42529A>G NG_008617.1:g.56387T>C LRG_487:g.42529A>G LRG_487t1:c.4952A>G P49815:p.Asn1651Ser - Protein change
- N1651S, N1407S, N1536S, N1608S, N1585S, N1584S, N1628S, N1548S, N1595S, N1607S
- Other names
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- Canonical SPDI
- NC_000016.10:2086833:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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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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- 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 | ||
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HI score
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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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TSC2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
11491 | 11719 |
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. |
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Likely pathogenic (2) |
no assertion criteria provided
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Aug 9, 2016 | RCV000042595.2 | |
Pathogenic (2) |
criteria provided, single submitter
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Feb 1, 2022 | RCV000359328.7 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Apr 1, 2024 | RCV000543686.10 | |
Pathogenic (1) |
criteria provided, single submitter
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May 15, 2017 | RCV002336159.2 |
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. |
More information
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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Pathogenic
(May 15, 2017)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002642642.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.N1651S pathogenic mutation (also known as c.4952A>G), located in coding exon 37 of the TSC2 gene, results from an A to G substitution at … (more)
The p.N1651S pathogenic mutation (also known as c.4952A>G), located in coding exon 37 of the TSC2 gene, results from an A to G substitution at nucleotide position 4952. The asparagine at codon 1651 is replaced by serine, an amino acid with highly similar properties. This mutation was detected as a de novo occurrence (paternity and maternity confirmed) in an individual who fulfilled diagnostic criteria for tuberous sclerosis complex (TSC). The mutation was also detected in this individual's two sons with TSC; however, it was not identified in his third unaffected son (Maheshwar MM et al. Hum. Mol. Genet., 1997 Oct;6:1991-6). In addition, this mutation has been detected in several individuals meeting formal diagnostic criteria for TSC (Jones AC et al. Am. J. Hum. Genet., 1999 May;64:1305-15; Dabora SL et al. Am. J. Hum. Genet., 2001 Jan;68:64-80; Langkau N et al. Eur. J. Pediatr., 2002 Jul;161:393-402; Zhao XY et al. Br. J. Dermatol., 2006 Nov;155:1070-3; Kamimura T et al. Epilepsia, 2006 Jun;47:991-7). In one other study, this mutation was shown to impair the ability of tuberin to act as a GTPase enhancing protein (Tee AR et al. Curr. Biol., 2003 Aug;13:1259-68). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Feb 01, 2022)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329791.7
First in ClinVar: Dec 06, 2016 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate a damaging effect as N1651S impairs the ability of tuberin to act as a GTPase activating protein (Tee et al., 2003); … (more)
Published functional studies demonstrate a damaging effect as N1651S impairs the ability of tuberin to act as a GTPase activating protein (Tee et al., 2003); Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 18032745, 11741833, 11112665, 18411301, 22055460, 12906785, 1846615, 27078846, 18550814, 15798777, 14718525, 21252315, 15024740, 9302281, 11521203, 27974549, 12111193, 10205261) (less)
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Pathogenic
(Nov 07, 2021)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 2
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV002041010.1
First in ClinVar: Dec 25, 2021 Last updated: Dec 25, 2021 |
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Pathogenic
(-)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 2
Affected status: yes
Allele origin:
germline
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Juno Genomics, Hangzhou Juno Genomics, Inc
Accession: SCV005417285.1
First in ClinVar: Nov 30, 2024 Last updated: Nov 30, 2024 |
Comment:
PM2_Supporting+PS4_Moderate+PS2+PP1+PP4+PP3_Moderate
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Pathogenic
(Apr 01, 2024)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 2
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000644583.6
First in ClinVar: Dec 26, 2017 Last updated: Feb 25, 2025 |
Comment:
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1651 of the TSC2 protein (p.Asn1651Ser). … (more)
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1651 of the TSC2 protein (p.Asn1651Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with tuberous sclerosis (PMID: 9302281, 12111193, 15024740). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 49335). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSC2 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects TSC2 function (PMID: 12906785, 14718525, 18411301, 18550814, 27078846). For these reasons, this variant has been classified as Pathogenic. (less)
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Likely pathogenic
(Aug 09, 2016)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: clinical testing
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Tuberous sclerosis syndrome
Affected status: yes
Allele origin:
germline
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Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital
Accession: SCV000805048.1
First in ClinVar: Sep 16, 2013 Last updated: Sep 16, 2013 |
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Pathogenic
(Mar 17, 2022)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV003839177.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
DNA sequence analysis of the TSC2 gene demonstrated a sequence change, c.4952A>G, in exon 38 that results in an amino acid change, p.Asn1651Ser. The p.Asn1651Ser … (more)
DNA sequence analysis of the TSC2 gene demonstrated a sequence change, c.4952A>G, in exon 38 that results in an amino acid change, p.Asn1651Ser. The p.Asn1651Ser change affects a highly conserved amino acid residue located in a domain of the TSC2 protein that is known to be functional. This sequence change has previously been described in multiple individuals with TSC2-related tuberous sclerosis complex (PMID: 9302281, 12111193, 15024740) and has not been described in population databases such as ExAC and gnomAD. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide mostly deleterious results for the p.Asn1651Ser substitution. Functional studies have demonstrated that this sequence change impacts the function of the TSC2 protein (PMID: 12906785, 18411301, 14718525, 18550814, 27078846). The p.Asn1651Ser amino acid change occurs in a region of the TSC2 gene where other missense sequence changes have been described in individuals with TSC2-related disorders including a missense change at the same position (p.Asn1651Thr, PMID: 32211034). Based on these evidences, this sequence change is classified as pathogenic. (less)
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not provided
(-)
N
Not contributing to aggregate classification
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no classification provided
Method: curation
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TSC
Affected status: yes
Allele origin:
germline
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Tuberous sclerosis database (TSC2)
Accession: SCV000066389.3
First in ClinVar: May 04, 2013 Last updated: Sep 16, 2013 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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mTORC1-mediated downregulation of COX2 restrains tumor growth caused by TSC2 deficiency. | Li H | Oncotarget | 2016 | PMID: 27078846 |
TSC1/TSC2 inactivation inhibits AKT through mTORC1-dependent up-regulation of STAT3-PTEN cascade. | Zha X | Cancer letters | 2011 | PMID: 22055460 |
Phospholipase D1 is an effector of Rheb in the mTOR pathway. | Sun Y | Proceedings of the National Academy of Sciences of the United States of America | 2008 | PMID: 18550814 |
The TSC1-TSC2 complex is required for proper activation of mTOR complex 2. | Huang J | Molecular and cellular biology | 2008 | PMID: 18411301 |
Two novel TSC2 mutations in Chinese patients with tuberous sclerosis complex and a literature review of 20 patients reported in China. | Zhao XY | The British journal of dermatology | 2006 | PMID: 17034546 |
Magnetoencephalography in patients with tuberous sclerosis and localization-related epilepsy. | Kamimura T | Epilepsia | 2006 | PMID: 16822245 |
Novel TSC2 mutations and decreased expression of tuberin in cultured tumor cells with an insertion mutation. | Feng JH | Human mutation | 2004 | PMID: 15024740 |
Tsc1+ and tsc2+ regulate arginine uptake and metabolism in Schizosaccharomyces pombe. | van Slegtenhorst M | The Journal of biological chemistry | 2004 | PMID: 14718525 |
Tuberous sclerosis complex gene products, Tuberin and Hamartin, control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb. | Tee AR | Current biology : CB | 2003 | PMID: 12906785 |
TSC1 and TSC2 mutations in tuberous sclerosis, the associated phenotypes and a model to explain observed TSC1/ TSC2 frequency ratios. | Langkau N | European journal of pediatrics | 2002 | PMID: 12111193 |
Tuberous sclerosis causing mutants of the TSC2 gene product affect proliferation and p27 expression. | Soucek T | Oncogene | 2001 | PMID: 11521203 |
Mutational analysis in a cohort of 224 tuberous sclerosis patients indicates increased severity of TSC2, compared with TSC1, disease in multiple organs. | Dabora SL | American journal of human genetics | 2001 | PMID: 11112665 |
Comprehensive mutation analysis of TSC1 and TSC2-and phenotypic correlations in 150 families with tuberous sclerosis. | Jones AC | American journal of human genetics | 1999 | PMID: 10205261 |
The GAP-related domain of tuberin, the product of the TSC2 gene, is a target for missense mutations in tuberous sclerosis. | Maheshwar MM | Human molecular genetics | 1997 | PMID: 9302281 |
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Text-mined citations for rs45517382 ...
HelpRecord last updated May 17, 2025
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.