chr1:58576805:G>A Detail (hg38) (TACSTD2)

Information

Genome

Assembly Position
hg19 chr1:59,042,477-59,042,477 View the variant detail on this assembly version.
hg38 chr1:58,576,805-58,576,805

HGVS

Type Transcript Protein
RefSeq NM_002353.2:c.352C>T NP_002344.2:p.Gln118Ter
Ensemble ENST00000371225.4:c.352C>T ENST00000371225.4:p.Gln118Ter
Summary

MGeND

Clinical significance
Variant entry
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 137290 OMIM
HGNC 11530 HGNC
Ensembl ENSG00000184292 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1668514 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 1999-04-01 no assertion criteria provided Lattice corneal dystrophy Type III germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Corneal dystrophy, Lattice type 3 Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P... BeFree 11004271 Detail
0.365 Corneal dystrophy, Lattice type 3 Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P... BeFree 11004271 Detail
0.365 Corneal dystrophy, Lattice type 3 NA CLINVAR Detail
0.365 Corneal dystrophy, Lattice type 3 More than 90% of GDLD patients possessed the same haplotype with a Q118X mutatio... BeFree 23038033 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002353.3(TACSTD2):c.352C>T (p.Gln118Ter) AND Lattice corneal dystrophy Type III ClinVar Detail
Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P501T of BIGH3 gene f... DisGeNET Detail
Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P501T of BIGH3 gene f... DisGeNET Detail
NA DisGeNET Detail
More than 90% of GDLD patients possessed the same haplotype with a Q118X mutation in TACSTD2. 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
rs80358223 dbSNP
Genome
hg38
Position
chr1:58,576,805-58,576,805
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1151
Mean of sample read depth (HGVD)
85.74
Standard deviation of sample read depth (HGVD)
41.17
Number of reference allele (HGVD)
2299
Number of alternative allele (HGVD)
3
Allele Frequency (HGVD)
0.0013032145960034753
Gene Symbol (HGVD)
TACSTD2
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))
rs80358223
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0007
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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