chr3:10142055:G>A Detail (hg38) (VHL)

Information

Genome

Assembly Position
hg19 chr3:10,183,739-10,183,739 View the variant detail on this assembly version.
hg38 chr3:10,142,055-10,142,055

HGVS

Type Transcript Protein
RefSeq NM_000551.3:c.208G>A NP_000542.1:p.Glu70Lys
NM_198156.2:c.208G>A NP_937799.1:p.Glu70Lys
Ensemble ENST00000256474.3:c.208G>A ENST00000256474.3:p.Glu70Lys
Summary

MGeND

Clinical significance Pathogenic
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:[No Data.]
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 608537 OMIM
HGNC 12687 HGNC
Ensembl ENSG00000134086 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other phakomatoses, not elsewhere classified germline MGS000077
(TMGS000152) 		Kenji Tamura Kochi University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2023-11-01 criteria provided, multiple submitters, no conflicts Von Hippel-Lindau syndrome germline unknown Detail
Likely pathogenic 2017-10-09 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2023-11-08 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Pathogenic 2023-11-08 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 9829912 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 25562111 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 25715769 Detail
von Hippel-Lindau disease C Diagnostic Supports Positive Rare Germline 3 25715769 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 24132471 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 27439424 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 25078357 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
0.658 Von Hippel-Lindau syndrome NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
Screening of 92 unrelated patients with VHL disease revealed 61 DNA variants. No variants were found... CIViC Evidence Detail
In the analysis of 63 clinically diagnosed VHL patients, 55 patients were found with pancreatic invo... CIViC Evidence Detail
A case report of a 74-year-old male with colorectal adenocarcinoma, clear cell renal cell carcinoma,... CIViC Evidence Detail
74-year-old man admitted to the Department of Neurosurgery at Yonsei University College of Medicine... CIViC Evidence Detail
Data was collected from 82 VHL mutation carriers in the Dutch VHL surveillance program. One patient ... CIViC Evidence Detail
Thirteen unrelated Korean subjects and their family members were tested for VHL mutations with direc... CIViC Evidence Detail
Medical records of 26 patients with germline mutations of the VHL gene who had been diagnosed with V... CIViC Evidence Detail
NM_000551.4(VHL):c.208G>A (p.Glu70Lys) AND Von Hippel-Lindau syndrome ClinVar Detail
NM_000551.4(VHL):c.208G>A (p.Glu70Lys) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000551.4(VHL):c.208G>A (p.Glu70Lys) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.208G>A (p.Glu70Lys) AND multiple conditions ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5030802 dbSNP
Genome
hg38
Position
chr3:10,142,055-10,142,055
Variant Type
snv
Reference Allele
G
Alternative Allele
A
East Asian Chromosome Counts (ExAC)
4972
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
67170
Allele Counts in All Race (ExAC)
1
Heterozygous Counts in All Race (ExAC)
1
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.4887598630340926E-5
Variant (CIViC) (CIViC Variant)
E70K (c.208G>A)
Transcript 1 (CIViC Variant)
ENST00000256474.2
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/1956
Summary (CIViC Variant)
The VHL gene has a low rate of benign missense variation and is known to be definitively associated with VHL disease. The E70K missense mutation, located in the Beta-domain of VHL, is rare in open-source genome databases (0.00001489 allele frequency in ExAC, 4.365e-6 allele frequency in gnomAD) and was identified in several individuals with VHL disease symptoms (see evidence statements). Thus, this variant could be assigned ACMG code 'PP2' - Missense mutation in a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease. Although this variant is registered once in ExAC and gnomAD, 'PM2' could be applied (Absent from controls in ESP, 1000 Genomes or ExAC) because VHL manifestations sometimes emerge later in adulthood. Thus, the allele may have been detected in a proband who was not yet affected by symptoms.
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