chr3:10146580:T>C Detail (hg38) (VHL, LOC107303340)

Information

Genome

Assembly Position
hg19 chr3:10,188,264-10,188,264 View the variant detail on this assembly version.
hg38 chr3:10,146,580-10,146,580

HGVS

Type Transcript Protein
RefSeq NM_000551.3:c.407T>C NP_000542.1:p.Phe136Ser
NM_198156.2:c.341-3207T>C
Ensemble ENST00000256474.3:c.407T>C ENST00000256474.3:p.Phe136Ser
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
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 COSM17996 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
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2023-07-19 criteria provided, multiple submitters, no conflicts Von Hippel-Lindau syndrome germline Detail
Pathogenic 2016-11-17 criteria provided, single submitter not provided germline Detail
Pathogenic 2022-11-02 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Pathogenic 2022-11-02 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 3 7987306 Detail
von Hippel-Lindau disease C Predisposing Supports Uncertain Significance Rare Germline 4 17024664 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 3 12624160 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 1 26763786 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
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
An investigation of 94 VHL patients without large deletions for intragenic mutations revealed 40 dif... CIViC Evidence Detail
Genotype-phenotype correlations of 573 VHL patients were analyzed and confirmed that higher risk of ... 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
Germline mutations were found in 20 Brazilian, VHL probands and their families. This missense mutati... CIViC Evidence Detail
Data was collected from 82 VHL mutation carriers in the Dutch VHL surveillance program. One patient ... CIViC Evidence Detail
A prospective study followed 128 participants affected by VHL syndrome for 12 years in Padova, Italy... CIViC Evidence Detail
NM_000551.4(VHL):c.407T>C (p.Phe136Ser) AND Von Hippel-Lindau syndrome ClinVar Detail
NM_000551.4(VHL):c.407T>C (p.Phe136Ser) AND not provided ClinVar Detail
NM_000551.4(VHL):c.407T>C (p.Phe136Ser) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.407T>C (p.Phe136Ser) AND multiple conditions ClinVar 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
rs5030833 dbSNP
Genome
hg38
Position
chr3:10,146,580-10,146,580
Variant Type
snv
Reference Allele
T
Alternative Allele
C
East Asian Chromosome Counts (ExAC)
8654
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)
121412
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)
8.236418146476461E-6
Variant (CIViC) (CIViC Variant)
F136S (c.407T>C)
Transcript 1 (CIViC Variant)
ENST
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/1801
Genome browser