chr3:10149822:C>T Detail (hg38) (VHL, LOC107303340)

Information

Genome

Assembly Position
hg19 chr3:10,191,506-10,191,506 View the variant detail on this assembly version.
hg38 chr3:10,149,822-10,149,822

HGVS

Type Transcript Protein
RefSeq NM_000551.3:c.499C>T NP_000542.1:p.Arg167Trp
NM_198156.2:c.376C>T NP_937799.1:p.Arg126Trp
Ensemble ENST00000256474.3:c.499C>T ENST00000256474.3:p.Arg167Trp
Summary

MGeND

Clinical significance Pathogenic
Variant entry 20
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 COSM14311 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000001
(TMGS000138) 		Kenjiro Kosaki Keio University
Pathogenic other phakomatoses, not elsewhere classified germline MGS000077
(TMGS000152) 		Kenji Tamura Kochi University
Pathogenic Von Hippel-Lindau Type 2 germline MGS000001
(TMGS000162) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2023-05-21 criteria provided, multiple submitters, no conflicts Von Hippel-Lindau syndrome germline unknown Detail
Pathogenic 2002-05-09 no assertion criteria provided pheochromocytoma germline Detail
Pathogenic 2022-06-15 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2022-05-25 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely pathogenic 2015-07-14 no assertion criteria provided Papillary renal cell carcinoma type 1 somatic Detail
Pathogenic 2023-12-06 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Pathogenic 2023-12-06 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Pathogenic 2021-10-01 criteria provided, single submitter nonpapillary renal cell carcinoma,pheochromocytoma,Von Hippel-Lindau syndrome,Chuvash polycythemia unknown Detail
Pathogenic 2021-10-01 criteria provided, single submitter nonpapillary renal cell carcinoma,pheochromocytoma,Von Hippel-Lindau syndrome,Chuvash polycythemia unknown Detail
Pathogenic 2021-10-01 criteria provided, single submitter nonpapillary renal cell carcinoma,pheochromocytoma,Von Hippel-Lindau syndrome,Chuvash polycythemia unknown Detail
Pathogenic 2021-10-01 criteria provided, single submitter nonpapillary renal cell carcinoma,pheochromocytoma,Von Hippel-Lindau syndrome,Chuvash polycythemia unknown Detail
Likely pathogenic 2024-04-04 criteria provided, single submitter Chuvash polycythemia germline Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 4 7728151 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 9829911 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 21463266 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 9829912 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 20660572 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 20846682 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 12624160 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 2 22357542 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 24132471 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 3 25867206 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
0.658 Von Hippel-Lindau syndrome NA CLINVAR Detail
0.125 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.416 pheochromocytoma NA CLINVAR Detail
0.416 pheochromocytoma Almost one fourth of patients with apparently sporadic pheochromocytoma may be c... UNIPROT 12000816 Detail
0.658 Von Hippel-Lindau syndrome The group of susceptibility genes for pheochromocytoma that included the proto-o... UNIPROT 12000816 Detail
Annotation

Annotations

DescrptionSourceLinks
In a study of 114 unrelated VHL families, 85 germline mutations were found. VHL mutations were detec... CIViC Evidence Detail
Germline mutations were found in all 93 families that fulfilled clinical criteria of VHL disease. Mu... CIViC Evidence Detail
In a study of 426 unrelated VHL patients, 111 were discovered to have alterations in the VHL gene. 1... CIViC Evidence Detail
Screening of 92 unrelated patients with VHL disease revealed 61 DNA variants. No variants were found... CIViC Evidence Detail
53 patients with a molecularly confirmed VHL mutation and a pancreatic neuroendocrine tumor were col... CIViC Evidence Detail
26 VHL patients from 18 families, who had undergone a partial adrenalectomy for pheochromocytoma wer... CIViC Evidence Detail
Germline mutations were found in 20 Brazilian, VHL probands and their families. This missense mutati... CIViC Evidence Detail
Mutational analysis for 16 patients with clinically diagnosed VHL disease, revealed 12 germline muta... CIViC Evidence Detail
Data was collected from 82 VHL mutation carriers in the Dutch VHL surveillance program. One patient ... CIViC Evidence Detail
Patients with ELSTs in the VHL registries of the participating centers in Europe were identified and... CIViC Evidence Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND Von Hippel-Lindau syndrome ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND Pheochromocytoma ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND not provided ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND Papillary renal cell carcinoma type 1 ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.499C>T (p.Arg167Trp) AND Chuvash polycythemia ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
Almost one fourth of patients with apparently sporadic pheochromocytoma may be carriers of mutations... DisGeNET Detail
The group of susceptibility genes for pheochromocytoma that included the proto-oncogene RET (associa... 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
rs5030820 dbSNP
Genome
hg38
Position
chr3:10,149,822-10,149,822
Variant Type
snv
Reference Allele
C
Alternative Allele
T
East Asian Chromosome Counts (ExAC)
8646
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)
121114
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)
8.256683785524381E-6
Variant (CIViC) (CIViC Variant)
R167W (c.499C>T)
Transcript 1 (CIViC Variant)
ENST00000256474.2
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/1747
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