ClinVar Genomic variation as it relates to human health
NM_000551.4(VHL):c.262T>A (p.Trp88Arg)
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.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000551.4(VHL):c.262T>A (p.Trp88Arg)
Variation ID: 456577 Accession: VCV000456577.14
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p25.3 3: 10142109 (GRCh38) [ NCBI UCSC ] 3: 10183793 (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 Mar 17, 2018 May 1, 2024 Jul 21, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000551.4:c.262T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000542.1:p.Trp88Arg missense NM_001354723.2:c.262T>A NP_001341652.1:p.Trp88Arg missense NM_198156.3:c.262T>A NP_937799.1:p.Trp88Arg missense NC_000003.12:g.10142109T>A NC_000003.11:g.10183793T>A NG_008212.3:g.5475T>A LRG_322:g.5475T>A LRG_322t1:c.262T>A LRG_322p1:p.Trp88Arg - Protein change
- W88R
- Other names
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- Canonical SPDI
- NC_000003.12:10142108:T:A
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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
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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
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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
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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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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VHL | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
832 | 2004 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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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Pathogenic (1) |
criteria provided, single submitter
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Dec 21, 2017 | RCV000558602.8 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Aug 1, 2018 | RCV000587190.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Apr 16, 2014 | RCV000679026.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 21, 2020 | RCV002431533.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 21, 2023 | RCV003459186.1 |
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
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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
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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
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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
(Feb 03, 2016)
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criteria provided, single submitter
Method: clinical testing
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Von Hippel-Lindau syndrome
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697493.1
First in ClinVar: Mar 17, 2018 Last updated: Mar 17, 2018 |
Comment:
Variant summary: This c.262T>A variant affects a conserved nucleotide, resulting in amino acid change from Trp to Arg in beta domain of VHL protein. 5/5 … (more)
Variant summary: This c.262T>A variant affects a conserved nucleotide, resulting in amino acid change from Trp to Arg in beta domain of VHL protein. 5/5 in-silico tools predict this variant to be damaging. This variant was not found in approximately 102226 control chromosomes including the large and broad populations from ExAC. This variant has been reported in at least ten independent VHL patients, two of whom carried the variant as somatic occurrence. In a family, the variant was found in two affected members, suggesting a possible cosegregation of the variant with disease (Glasker_2001). Another nucleotide change leading to the same amino acid change c.262T>C is a pathogenic variant, a strong evidence that this nucleotide change is also pathogenic. In addition, codon 88 is a mutational hot spot in which other potentially pathogenic variants such as .W88C, p.W88S, p.W88* (c.263G>A) and p.W88* (c.264G>A) have been reported in VHL disease or its related cancers. Taken together, this variant has been classified as a Pathogenic. (less)
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Pathogenic
(Apr 16, 2014)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV000805333.1
First in ClinVar: Sep 14, 2018 Last updated: Sep 14, 2018 |
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Pathogenic
(Aug 01, 2018)
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criteria provided, single submitter
Method: clinical testing
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von Hippel-Lindau syndrome
Affected status: yes
Allele origin:
germline
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Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000897793.1
First in ClinVar: Apr 17, 2019 Last updated: Apr 17, 2019 |
Number of individuals with the variant: 6
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Pathogenic
(Jul 21, 2023)
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criteria provided, single submitter
Method: clinical testing
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Chuvash polycythemia
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004208763.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Dec 21, 2017)
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criteria provided, single submitter
Method: clinical testing
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Von Hippel-Lindau syndrome
Chuvash polycythemia
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000626889.5
First in ClinVar: Dec 26, 2017 Last updated: Feb 28, 2024 |
Comment:
A different variant (c.262T>C) giving rise to the same protein effect observed here (p.Trp88Arg) has been reported in individuals affected with Von Hippel-Lindau syndrome (PMID: … (more)
A different variant (c.262T>C) giving rise to the same protein effect observed here (p.Trp88Arg) has been reported in individuals affected with Von Hippel-Lindau syndrome (PMID: 12624160, 17688370, Invitae). In addition, a different missense substitution at this codon (p.Trp88Cys) has been determined to be likely pathogenic (PMID: 10567493, 21715564). This suggests that the tryptophan residue is critical for VHL protein function and that other missense substitutions at this position may also be pathogenic. For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This sequence change replaces tryptophan with arginine at codon 88 of the VHL protein (p.Trp88Arg). The tryptophan residue is highly conserved and there is a moderate physicochemical difference between tryptophan and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in several individuals affected with Von Hippel-Lindau syndrome (PMID: 10567493, 7728151, 17024664, 8956040). (less)
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Pathogenic
(Aug 21, 2020)
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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: SCV002743251.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.W88R variant (also known as c.262T>A), located in coding exon 1 of the VHL gene, results from a T to A substitution at nucleotide … (more)
The p.W88R variant (also known as c.262T>A), located in coding exon 1 of the VHL gene, results from a T to A substitution at nucleotide position 262. The tryptophan at codon 88 is replaced by arginine, an amino acid with dissimilar properties. This alteration (also designated 475T>A) was detected in multiple patients who met clinical criteria or presented with clinical features of Von Hippel-Lindau (VHL) Syndrome (Chen F et al. Hum. Mutat., 1995;5:66-75; Gläsker S et al. J. Neurol. Neurosurg. Psychiatry, 1999 Dec;67:758-62; Jilg CA et al. Urol. Int., 2012 Dec;88:71-8; Ong KR et al. Hum. Mutat., 2007 Feb;28:143-9; Rocha JC et al. J. Med. Genet., 2003 Mar;40:e31; Stanojevic BR et al. Neoplasma, 2007;54:402-6; Zbar B et al. Hum. Mutat., 1996;8:348-57). In addition, a similar alteration resulting in the same amino acid change (W88R) but with a different nucleotide change (c.262T>C) has been reported in VHL patients (Hong B et al. Front Genet, 2019 Sep;10:867; Kim WT et al. J. Korean Med. Sci., 2009 Dec;24:1145-9). Based on internal structural analysis, W88R is at a putative HIF1 binding interface and the variant is moderately destabilizing to the local structure and more disruptive than known variants in the region (Shmueli MD et al. PLoS ONE, 2014 Oct;9:e109864; Van Molle I et al. Chem. Biol., 2012 Oct;19:1300-12). This amino acid position is highly 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)
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Pathogenic
(Oct 16, 2019)
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no assertion criteria provided
Method: clinical testing
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Von Hippel-Lindau syndrome
Affected status: unknown
Allele origin:
germline
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Clinical Genomics Labs, University Health Network
Accession: SCV001950153.1
First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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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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Frequent Mutations of VHL Gene and the Clinical Phenotypes in the Largest Chinese Cohort With Von Hippel-Lindau Disease. | Hong B | Frontiers in genetics | 2019 | PMID: 31620170 |
In silico VHL Gene Mutation Analysis and Prognosis of Pancreatic Neuroendocrine Tumors in von Hippel-Lindau Disease. | Tirosh A | The Journal of clinical endocrinology and metabolism | 2018 | PMID: 29294023 |
Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome. | Shmueli MD | PloS one | 2014 | PMID: 25310726 |
Germline mutation of Glu70Lys is highly frequent in Korean patients with von Hippel-Lindau (VHL) disease. | Hwang S | Journal of human genetics | 2014 | PMID: 25078357 |
Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. | Van Molle I | Chemistry & biology | 2012 | PMID: 23102223 |
Growth kinetics in von Hippel-Lindau-associated renal cell carcinoma. | Jilg CA | Urologia internationalis | 2012 | PMID: 22156657 |
Effects of point mutations in pVHL on the binding of HIF-1α. | Domene C | Proteins | 2012 | PMID: 22105711 |
VHL gene mutations and their effects on hypoxia inducible factor HIFα: identification of potential driver and passenger mutations. | Rechsteiner MP | Cancer research | 2011 | PMID: 21715564 |
Analysis of VHL Gene Alterations and their Relationship to Clinical Parameters in Sporadic Conventional Renal Cell Carcinoma. | Young AC | Clinical cancer research : an official journal of the American Association for Cancer Research | 2009 | PMID: 19996202 |
Clinical characteristics of renal cell carcinoma in Korean patients with von Hippel-Lindau disease compared to sporadic bilateral or multifocal renal cell carcinoma. | Kim WT | Journal of Korean medical science | 2009 | PMID: 19949673 |
Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis. | Forman JR | Proteins | 2009 | PMID: 19408298 |
Germline VHL gene mutations in three Serbian families with von Hippel-Lindau disease. | Stanojevic BR | Neoplasma | 2007 | PMID: 17688370 |
Genotype-phenotype correlations in von Hippel-Lindau disease. | Ong KR | Human mutation | 2007 | PMID: 17024664 |
Genetic and epigenetic analysis of von Hippel-Lindau (VHL) gene alterations and relationship with clinical variables in sporadic renal cancer. | Banks RE | Cancer research | 2006 | PMID: 16488999 |
High frequency of novel germline mutations in the VHL gene in the heterogeneous population of Brazil. | Rocha JC | Journal of medical genetics | 2003 | PMID: 12624160 |
Comprehensive mutational analysis of the VHL gene in sporadic renal cell carcinoma: relationship to clinicopathological parameters. | Kondo K | Genes, chromosomes & cancer | 2002 | PMID: 11921283 |
Reconsideration of biallelic inactivation of the VHL tumour suppressor gene in hemangioblastomas of the central nervous system. | Gläsker S | Journal of neurology, neurosurgery, and psychiatry | 2001 | PMID: 11309459 |
Clinical and genetic analysis of patients with pancreatic neuroendocrine tumors associated with von Hippel-Lindau disease. | Libutti SK | Surgery | 2000 | PMID: 11114638 |
The impact of molecular genetic analysis of the VHL gene in patients with haemangioblastomas of the central nervous system. | Gläsker S | Journal of neurology, neurosurgery, and psychiatry | 1999 | PMID: 10567493 |
Improved detection of germline mutations in the von Hippel-Lindau disease tumor suppressor gene. | Stolle C | Human mutation | 1998 | PMID: 9829911 |
Genotype-phenotype correlations in von Hippel-Lindau disease. | Neumann HP | Journal of internal medicine | 1998 | PMID: 9681856 |
Germline mutations in the Von Hippel-Lindau disease (VHL) gene in families from North America, Europe, and Japan. | Zbar B | Human mutation | 1996 | PMID: 8956040 |
Germline mutations in the von Hippel-Lindau disease tumor suppressor gene: correlations with phenotype. | Chen F | Human mutation | 1995 | PMID: 7728151 |
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Text-mined citations for rs1553619431 ...
HelpRecord last updated Sep 29, 2024
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.