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NM_000551.3(VHL):c.293A>C (p.Tyr98Ser)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Feb 4, 2019
Accession:
VCV000219160.3
Variation ID:
219160
Description:
single nucleotide variant
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NM_000551.3(VHL):c.293A>C (p.Tyr98Ser)

Allele ID
217068
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.3
Genomic location
3: 10142140 (GRCh38) GRCh38 UCSC
3: 10183824 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.10183824A>C
NC_000003.12:g.10142140A>C
NM_000551.3:c.293A>C NP_000542.1:p.Tyr98Ser missense
... more HGVS
Protein change
Y98S
Other names
-
Canonical SPDI
NC_000003.12:10142139:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA279916
dbSNP: rs864321643
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Feb 4, 2019 RCV001064921.2
Likely pathogenic 1 no assertion criteria provided Dec 1, 2015 RCV000203508.1
Uncertain significance 1 no assertion criteria provided Feb 26, 2016 RCV000208847.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
VHL Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
551 1350

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Feb 04, 2019)
criteria provided, single submitter
Method: clinical testing
Von Hippel-Lindau syndrome
Erythrocytosis, familial, 2
Allele origin: germline
Invitae
Accession: SCV001229857.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (10)
Comment:
This sequence change replaces tyrosine with serine at codon 98 of the VHL protein (p.Tyr98Ser). The tyrosine residue is highly conserved and there is a … (more)
Likely pathogenic
(Dec 01, 2015)
no assertion criteria provided
Method: research
Pheochromocytoma
(Autosomal dominant inheritance)
Allele origin: germline
Endocrinology Clinic, Seth G.S. Medical College
Study: Spectrum of Germline Mutations in Indian Patients with Pheochromocytoma/ Paraganglioma (PHEO/PGL)
Accession: SCV000258643.1
Submitted: (Jan 01, 2016)
Evidence details
Uncertain significance
(Feb 26, 2016)
no assertion criteria provided
Method: clinical testing
Von Hippel-Lindau syndrome
Allele origin: germline
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia
Accession: SCV000264697.1
Submitted: (Mar 02, 2016)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Genotype phenotype correlation in Asian Indian von Hippel-Lindau (VHL) syndrome patients with pheochromocytoma/paraganglioma. Lomte N Familial cancer 2018 PMID: 29124493
Genotype-phenotype correlations in Chinese von Hippel-Lindau disease patients. Peng S Oncotarget 2017 PMID: 28388566
Germline mutations and genotype-phenotype correlation in Asian Indian patients with pheochromocytoma and paraganglioma. Pandit R European journal of endocrinology 2016 PMID: 27539324
Genotype-phenotype correlations of pheochromocytoma in two large von Hippel-Lindau (VHL) type 2A kindreds with different missense mutations. Nielsen SM American journal of medical genetics. Part A 2011 PMID: 21204227
The Warburg effect is genetically determined in inherited pheochromocytomas. Favier J PloS one 2009 PMID: 19763184
Head and neck paragangliomas in von Hippel-Lindau disease and multiple endocrine neoplasia type 2. Boedeker CC The Journal of clinical endocrinology and metabolism 2009 PMID: 19336503
VHL c.505 T>C mutation confers a high age related penetrance but no increased overall mortality. Bender BU Journal of medical genetics 2001 PMID: 11483638
Mutations of the VHL gene in sporadic renal cell carcinoma: definition of a risk factor for VHL patients to develop an RCC. Gallou C Human mutation 1999 PMID: 10408776
Von Hippel-Lindau (VHL) disease with pheochromocytoma in the Black Forest region of Germany: evidence for a founder effect. Brauch H Human genetics 1995 PMID: 7759077
Germline mutations in the von Hippel-Lindau disease tumor suppressor gene: correlations with phenotype. Chen F Human mutation 1995 PMID: 7728151

Text-mined citations for rs864321643...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 10, 2021