chr12:102158009:T> Detail (hg19) (GNPTAB)

Information

Genome

Assembly Position
hg19 chr12:102,158,009-102,158,009
hg38 chr12:101,764,231-101,764,231 

HGVS

Type Transcript Protein
RefSeq NM_024312.4:c.2686delA NP_077288.2:p.Lys898SerfsTer13
Ensemble ENST00000299314.12:c.2686delA ENST00000299314.12:p.Lys898SerfsTer13
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 607840 OMIM
HGNC 29670 HGNC
Ensembl ENSG00000111670 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv47015934 TogoVar
COSMIC COSM1358184 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2016-07-28 criteria provided, single submitter Pseudo-Hurler polydystrophy germline unknown Detail
Pathogenic Likely pathogenic 2023-03-21 criteria provided, multiple submitters, no conflicts Pseudo-Hurler polydystrophy,Mucolipidosis type II germline unknown Detail
Pathogenic Likely pathogenic 2023-03-21 criteria provided, multiple submitters, no conflicts Pseudo-Hurler polydystrophy,Mucolipidosis type II germline unknown Detail
Pathogenic 2021-07-10 criteria provided, single submitter not provided germline Detail
Pathogenic no assertion criteria provided mucolipidosis inherited Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.480 Pseudo-Hurler polydystrophy NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND Pseudo-Hurler polydystrophy ClinVar Detail
NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND multiple conditions ClinVar Detail
NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND multiple conditions ClinVar Detail
NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND not provided ClinVar Detail
NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND Mucolipidosis 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
rs281864999 dbSNP
Genome
hg19
Position
chr12:102,158,009-102,158,009
Variant Type
snv
Reference Allele
T
Alternative Allele
-
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1199
Mean of sample read depth (HGVD)
41.02
Standard deviation of sample read depth (HGVD)
39.02
Number of reference allele (HGVD)
2397
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.170141784820684E-4
Gene Symbol (HGVD)
GNPTAB
Genome browser