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NM_000551.3(VHL):c.487C>T (p.Leu163Phe)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Aug 5, 2021)
Last evaluated:
Jul 12, 2021
Accession:
VCV000480772.6
Variation ID:
480772
Description:
single nucleotide variant
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NM_000551.3(VHL):c.487C>T (p.Leu163Phe)

Allele ID
473349
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.3
Genomic location
3: 10149810 (GRCh38) GRCh38 UCSC
3: 10191494 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.10191494C>T
NC_000003.12:g.10149810C>T
NM_000551.3:c.487C>T NP_000542.1:p.Leu163Phe missense
... more HGVS
Protein change
L163F, L122F
Other names
-
Canonical SPDI
NC_000003.12:10149809:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA351756135
dbSNP: rs1553620318
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter May 2, 2018 RCV000561095.2
Uncertain significance 1 criteria provided, single submitter Jun 9, 2019 RCV001224534.1
Uncertain significance 1 criteria provided, single submitter Jul 12, 2021 RCV001553667.1
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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
LOC107303340 - - - GRCh38 - 774

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 02, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000664462.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (5)
Comment:
The p.L163F variant (also known as c.487C>T), located in coding exon 3 of the VHL gene, results from a C to T substitution at nucleotide … (more)
Uncertain significance
(Jun 09, 2019)
criteria provided, single submitter
Method: clinical testing
Von Hippel-Lindau syndrome
Erythrocytosis, familial, 2
Allele origin: germline
Invitae
Accession: SCV001396738.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces leucine with phenylalanine at codon 163 of the VHL protein (p.Leu163Phe). The leucine residue is highly conserved and there is a … (more)
Uncertain significance
(Jul 12, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001774604.1
Submitted: (Aug 05, 2021)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: VHL c.487C>T (p.Leu163Phe) results in a non-conservative amino acid change located in the von Hippel-Lindau disease tumour suppressor, beta/alpha domain (IPR022772) of the … (more)

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
ISOLATED PARAGANGLIOMA IN A PATIENT WITH <i>VHL P.L163F</i> MUTATION. Goldstein M AACE clinical case reports 2020 PMID: 32671223
Genotype phenotype correlation in Asian Indian von Hippel-Lindau (VHL) syndrome patients with pheochromocytoma/paraganglioma. Lomte N Familial cancer 2018 PMID: 29124493
Germline mutations and genotype-phenotype correlation in Asian Indian patients with pheochromocytoma and paraganglioma. Pandit R European journal of endocrinology 2016 PMID: 27811160
Germline mutations and genotype-phenotype correlation in Asian Indian patients with pheochromocytoma and paraganglioma. Pandit R European journal of endocrinology 2016 PMID: 27539324
Clinical and genetic investigation of a multi-generational Chinese family afflicted with Von Hippel-Lindau disease. Zhang J Chinese medical journal 2015 PMID: 25563310
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
Improved detection of germline mutations in Korean VHL patients by multiple ligation-dependent probe amplification analysis. Cho HJ Journal of Korean medical science 2009 PMID: 19270817
von Hippel-Lindau gene mutation in non-syndromic familial pheochromocytomas. Tong AL Annals of the New York Academy of Sciences 2006 PMID: 17102088
Familial isolated pheochromocytoma presenting a new mutation in the von Hippel-Lindau gene. Sansó G American journal of hypertension 2004 PMID: 15607616

Text-mined citations for rs1553620318...

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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 Aug 11, 2021