chr12:102163963:A>G Detail (hg19) (GNPTAB)

Information

Genome

Assembly Position
hg19 chr12:102,163,963-102,163,963
hg38 chr12:101,770,185-101,770,185 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_024312.4:c.1120T>C NP_077288.2:p.Phe374Leu
Ensemble ENST00000549940.5:c.1120T>C ENST00000549940.5:p.Phe374Leu
ENST00000299314.12:c.1120T>C ENST00000299314.12:p.Phe374Leu
Summary

MGeND

Clinical significance Likely pathogenic Pathogenic
Variant entry 5
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance 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 tgv47016373 TogoVar
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
Pathogenic other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Likely pathogenic other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Likely pathogenic other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2009-03-01 no assertion criteria provided Pseudo-Hurler polydystrophy germline Detail
Pathogenic 2009-03-01 no assertion criteria provided Mucolipidosis type II germline unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.480 Pseudo-Hurler polydystrophy NA CLINVAR Detail
0.441 MUCOLIPIDOSIS II ALPHA/BETA (disorder) NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_024312.5(GNPTAB):c.1120T>C (p.Phe374Leu) AND Pseudo-Hurler polydystrophy ClinVar Detail
NM_024312.5(GNPTAB):c.1120T>C (p.Phe374Leu) AND Mucolipidosis type II ClinVar Detail
NA DisGeNET 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
rs137852900 dbSNP
Genome
hg19
Position
chr12:102,163,963-102,163,963
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
81.64
Standard deviation of sample read depth (HGVD)
39.67
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
GNPTAB
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs137852900
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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