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NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND VHL-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 23, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003415985.5

Allele description [Variation Report for NM_000551.4(VHL):c.154G>A (p.Glu52Lys)]

NM_000551.4(VHL):c.154G>A (p.Glu52Lys)

Gene:
VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_000551.4(VHL):c.154G>A (p.Glu52Lys)
Other names:
NM_000551.4(VHL):c.154G>A
HGVS:
  • NC_000003.12:g.10142001G>A
  • NG_008212.3:g.5367G>A
  • NM_000551.4:c.154G>AMANE SELECT
  • NM_001354723.2:c.154G>A
  • NM_198156.3:c.154G>A
  • NP_000542.1:p.Glu52Lys
  • NP_000542.1:p.Glu52Lys
  • NP_001341652.1:p.Glu52Lys
  • NP_937799.1:p.Glu52Lys
  • LRG_322t1:c.154G>A
  • LRG_322:g.5367G>A
  • LRG_322p1:p.Glu52Lys
  • NC_000003.11:g.10183685G>A
  • NM_000551.3:c.154G>A
  • P40337:p.Glu52Lys
Protein change:
E52K
Links:
UniProtKB: P40337#VAR_005671; dbSNP: rs373068386
NCBI 1000 Genomes Browser:
rs373068386
Molecular consequence:
  • NM_000551.4:c.154G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354723.2:c.154G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198156.3:c.154G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
VHL-related disorder
Synonyms:
VHL-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004116597PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Uncertain significance
(Jul 23, 2024)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004116597.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The VHL c.154G>A variant is predicted to result in the amino acid substitution p.Glu52Lys. This variant has been reported in patients with von Hippel-Lindau disease with and without renal involvement (Dollfus et al. 2002. PubMed ID: 12202531; Supplementary Table S1, Gallou et al. 2004. PubMed ID: 15300849). In addition, this variant has been identified and classified as a variant of uncertain significance in a study analyzing incidental findings in patients of European and African-ancestry that participated in the National Heart, Lung, and Blood Institute Exome Sequencing Project (Supplementary Table 1, Amendola et al. 2015. PubMed ID: 25637381; Supplementary Table 1, Dorschner et al. 2013. PubMed ID: 24055113). This variant has also been reported in an individual with hepatoblastoma (Aguiar et al. 2022. PubMed ID: 35495172). However, this variant is reported in 0.075% of alleles in individuals of African descent in gnomAD, which may be too common to be a primary cause of disease. This variant has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/161402/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024