chr3:10142001:G>A Detail (hg38) (VHL)

Information

Genome

Assembly Position
hg19 chr3:10,183,685-10,183,685 View the variant detail on this assembly version.
hg38 chr3:10,142,001-10,142,001

HGVS

Type Transcript Protein
RefSeq NM_000551.3:c.154G>A NP_000542.1:p.Glu52Lys
NM_198156.2:c.154G>A NP_937799.1:p.Glu52Lys
Ensemble ENST00000256474.3:c.154G>A ENST00000256474.3:p.Glu52Lys
Summary

MGeND

Clinical significance
Variant entry
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 Conflicting classifications of pathogenicity
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 tgv316381738 TogoVar
COSMIC COSM1417286 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2023-11-20 criteria provided, conflicting interpretations Von Hippel-Lindau syndrome unknown germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Chuvash polycythemia,Von Hippel-Lindau syndrome germline Detail
Likely benign 2021-06-18 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Conflicting interpretations of pathogenicity 2023-06-01 criteria provided, conflicting interpretations not provided germline Detail
no classifications from unflagged records 2023-10-26 no classifications from unflagged records hepatoblastoma germline Detail
Uncertain significance 2023-08-15 criteria provided, single submitter not specified germline Detail
no classifications from unflagged records 2023-10-26 no classifications from unflagged records Enchondromatosis unknown Detail
Uncertain significance 2022-12-22 criteria provided, single submitter VHL-related disorder 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 9829912 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
0.125 Neoplastic Syndromes, Hereditary 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
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND Von Hippel-Lindau syndrome ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND multiple conditions ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND not provided ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND Hepatoblastoma ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND not specified ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND Enchondromatosis ClinVar Detail
NM_000551.4(VHL):c.154G>A (p.Glu52Lys) AND VHL-related disorder 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
rs373068386 dbSNP
Genome
hg38
Position
chr3:10,142,001-10,142,001
Variant Type
snv
Reference Allele
G
Alternative Allele
A
East Asian Chromosome Counts (ExAC)
1306
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)
24038
Allele Counts in All Race (ExAC)
5
Heterozygous Counts in All Race (ExAC)
5
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.080039936766786E-4
Variant (CIViC) (CIViC Variant)
E52K (c.154G>A)
Transcript 1 (CIViC Variant)
ENST00000256474.2
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/1734
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