NM_000546.6(TP53):c.476C>T (p.Ala159Val)
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
Pathogenic (2); Likely pathogenic (4)
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.
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
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NM_000546.6(TP53):c.476C>T (p.Ala159Val)
Variation ID: 458545 Accession: VCV000458545.18
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 17p13.1 17: 7675136 (GRCh38) [ NCBI UCSC ] 17: 7578454 (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 May 26, 2018 Feb 23, 2026 Oct 12, 2025 Somatic - Clinical impact Nov 22, 2025 Nov 22, 2025 Jul 6, 2023 Somatic - Oncogenicity Aug 11, 2024 Mar 11, 2025 Mar 4, 2025 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000546.6:c.476C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000537.3:p.Ala159Val missense NM_000546.4:c.476C>T NM_001126112.3:c.476C>T NP_001119584.1:p.Ala159Val missense NM_001126113.3:c.476C>T NP_001119585.1:p.Ala159Val missense NM_001126114.3:c.476C>T NP_001119586.1:p.Ala159Val missense NM_001126115.2:c.80C>T NP_001119587.1:p.Ala27Val missense NM_001126116.2:c.80C>T NP_001119588.1:p.Ala27Val missense NM_001126117.2:c.80C>T NP_001119589.1:p.Ala27Val missense NM_001126118.2:c.359C>T NP_001119590.1:p.Ala120Val missense NM_001276695.3:c.359C>T NP_001263624.1:p.Ala120Val missense NM_001276696.3:c.359C>T NP_001263625.1:p.Ala120Val missense NM_001276697.3:c.-2C>T 5 prime UTR NM_001276698.3:c.-2C>T 5 prime UTR NM_001276699.3:c.-2C>T 5 prime UTR NM_001276760.3:c.359C>T NP_001263689.1:p.Ala120Val missense NM_001276761.3:c.359C>T NP_001263690.1:p.Ala120Val missense NM_001407262.1:c.476C>T NP_001394191.1:p.Ala159Val missense NM_001407263.1:c.359C>T NP_001394192.1:p.Ala120Val missense NM_001407264.1:c.476C>T NP_001394193.1:p.Ala159Val missense NM_001407265.1:c.359C>T NP_001394194.1:p.Ala120Val missense NM_001407266.1:c.476C>T NP_001394195.1:p.Ala159Val missense NM_001407267.1:c.359C>T NP_001394196.1:p.Ala120Val missense NM_001407268.1:c.476C>T NP_001394197.1:p.Ala159Val missense NM_001407269.1:c.359C>T NP_001394198.1:p.Ala120Val missense NM_001407270.1:c.476C>T NP_001394199.1:p.Ala159Val missense NM_001407271.1:c.359C>T NP_001394200.1:p.Ala120Val missense NR_176326.1:n.618C>T non-coding transcript variant NC_000017.11:g.7675136G>A NC_000017.10:g.7578454G>A NG_017013.2:g.17415C>T LRG_321:g.17415C>T LRG_321t1:c.476C>T LRG_321p1:p.Ala159Val LRG_321t2:c.476C>T LRG_321:p.Ala159Val LRG_321t3:c.476C>T LRG_321p3:p.Ala159Val LRG_321t4:c.476C>T LRG_321p4:p.Ala159Val LRG_321t5:c.80C>T LRG_321p5:p.Ala27Val LRG_321t6:c.80C>T LRG_321p6:p.Ala27Val LRG_321t7:c.80C>T LRG_321p7:p.Ala27Val LRG_321t8:c.359C>T LRG_321p8:p.Ala120Val - Protein change
- A120V, A159V, A27V
- Other names
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- Canonical SPDI
- NC_000017.11:7675135:G:A
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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 | ||
|---|---|---|---|---|---|---|
| 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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| TP53 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3915 | 4016 | |
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. |
|---|---|---|---|---|
| Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Oct 12, 2025 | RCV000527533.11 | |
| Likely pathogenic (1) |
criteria provided, single submitter
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Sep 29, 2021 | RCV001764539.2 | |
| Pathogenic (1) |
criteria provided, single submitter
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Apr 28, 2025 | RCV002341276.3 | |
| Likely pathogenic (1) |
criteria provided, single submitter
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Mar 21, 2023 | RCV003476227.1 | |
| Likely pathogenic (1) |
criteria provided, single submitter
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Feb 14, 2024 | RCV004023788.1 |
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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Likely pathogenic
(Sep 29, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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not provided |
GeneDx
Accession: SCV002008431.2
First in ClinVar: Nov 06, 2021 Last updated: Mar 04, 2023 |
Comment:
show
Published functional studies demonstrate a damaging effect: non-functional transactivation and impaired growth suppression activities (Kato 2003, Kotler 2018).; Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17724467, 20505364, 22862161, 12826609, 16322298, 29979965, 15510160) (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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|
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Pathogenic
(Oct 12, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Li-Fraumeni syndrome |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000629826.9
First in ClinVar: Dec 26, 2017 Last updated: Feb 23, 2026 |
Comment:
show
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 159 of the TP53 protein (p.Ala159Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of Li-Fraumeni syndrome (internal data). ClinVar contains an entry for this variant (Variation ID: 458545). Invitae Evidence Modeling incorporating data from in vitro experimental studies (PMID: 12826609, 29979965, 30224644) indicates that this missense variant is expected to disrupt TP53 function with a positive predictive value of 97.5%. Experimental studies have shown that this missense change affects TP53 function (PMID: 12826609, 29979965, 30224644). This variant disrupts the p.Ala159 amino acid residue in TP53. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27545002, 29070607, 32658383). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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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Likely pathogenic
(Mar 21, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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Adrenocortical carcinoma, hereditary |
Baylor Genetics
Accession: SCV004204254.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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
(Feb 14, 2024)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Li-Fraumeni syndrome 1 |
Myriad Genetics, Inc.
Accession: SCV004932438.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
show
This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 20505364, 29979965]. This variant is expected to disrupt protein structure [Myriad internal data]. (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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Pathogenic
(Apr 28, 2025)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Hereditary cancer-predisposing syndrome |
Ambry Genetics
Accession: SCV002638661.3
First in ClinVar: Nov 29, 2022 Last updated: Jul 13, 2025 |
Comment:
show
The p.A159V pathogenic mutation (also known as c.476C>T), located in coding exon 4 of the TP53 gene, results from a C to T substitution at nucleotide position 476. The alanine at codon 159 is replaced by valine, an amino acid with similar properties. This variant is in the DNA binding domain of the TP53 protein and is reported to have non-functional transactivation in yeast based assays (Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100:8424-9). Studies conducted in human cell lines indicate this alteration is deficient at growth suppression and has a dominant negative effect (Kotler E et al. Mol.Cell. 2018 Jul;71:178-190.e8; Giacomelli AO et al. Nat. Genet. 2018 Oct;50:1381-1387). This alteration has been observed numerous times as a somatic mutation in the cancerhotspots.org database (Chang MT et al. Cancer Discov. 2018 02;8:174-183). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (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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Likely Pathogenic
(Jun 16, 2023)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Li-Fraumeni syndrome |
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital
Accession: SCV007449424.1
First in ClinVar: Feb 15, 2026 Last updated: Feb 15, 2026 |
Comment:
show
Well-established functional studies have demonstrated this variant to have a damaging effect on protein function or splicing (ACMG/AMP: PS3). This variant is located in a mutational hot spot and/or critical and well-established functional domain (ACMG/AMP: PM1). This variant is absent from or present at an exceedingly low frequency in gnomAD, a large-scale control population database (ACMG/AMP: PM2_Supporting). (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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Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Rhabdomyosarcoma associated with germline TP53 alteration in children and adolescents: The French experience. | Pondrom M | Pediatric blood & cancer | 2020 | PMID: 32658383 |
| Mutational processes shape the landscape of TP53 mutations in human cancer. | Giacomelli AO | Nature genetics | 2018 | PMID: 30224644 |
| A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. | Kotler E | Molecular cell | 2018 | PMID: 29979965 |
| Contribution of de novo and mosaic TP53 mutations to Li-Fraumeni syndrome. | Renaux-Petel M | Journal of medical genetics | 2018 | PMID: 29070607 |
| Prevalence of low-penetrant germline TP53 D49H mutation in Japanese cancer patients. | Yamaguchi K | Biomedical research (Tokyo, Japan) | 2016 | PMID: 27545002 |
| Transactivation by temperature-dependent p53 mutants in yeast and human cells. | Slovackova J | Cell cycle (Georgetown, Tex.) | 2010 | PMID: 20505364 |
| Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. | Kato S | Proceedings of the National Academy of Sciences of the United States of America | 2003 | PMID: 12826609 |
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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Oncogenic
criteria provided, single submitter
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Mar 4, 2025 | RCV004669032.2 | ||
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Tier I (Strong)
- diagnostic
- supports diagnosis
(1)
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Jul 6, 2023 | RCV006254099.1 |
Submissions - Somatic
|
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)
- Diagnostic
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supports diagnosis (Jul 06, 2023)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Embryonal rhabdomyosarcoma |
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital
Accession: SCV007105370.1
First In ClinVar: Nov 22, 2025 Last updated: Nov 22, 2025 |
Comment:
show
Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in embryonal rhabdomyosarcoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant. 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 24436047, 34166060, 24332040, 25768946, 26138366). (less)
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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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
|
criteria provided, single submitter
|
Neoplasm |
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV005094446.2
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 |
|---|---|---|---|---|
| Genomic Classification and Clinical Outcome in Rhabdomyosarcoma: A Report From an International Consortium. | Shern JF | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2021 | PMID: 34166060 |
| A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. | Kotler E | Molecular cell | 2018 | PMID: 29979965 |
| Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. | Seki M | Nature communications | 2015 | PMID: 26138366 |
| Clonality and evolutionary history of rhabdomyosarcoma. | Chen L | PLoS genetics | 2015 | PMID: 25768946 |
| Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. | Shern JF | Cancer discovery | 2014 | PMID: 24436047 |
| Targeting oxidative stress in embryonal rhabdomyosarcoma. | Chen X | Cancer cell | 2013 | PMID: 24332040 |
| Roscovitine-induced apoptosis of H1299 cells depends on functional status of p53. | Slovackova J | Neoplasma | 2012 | PMID: 22862161 |
| Transactivation by temperature-dependent p53 mutants in yeast and human cells. | Slovackova J | Cell cycle (Georgetown, Tex.) | 2010 | PMID: 20505364 |
Text-mined citations for rs1555526131 ...
HelpRecord last updated Apr 13, 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.
