chr2:43872294:C>A Detail (hg38) (ABCG8)

Information

Genome

Assembly Position
hg19 chr2:44,099,433-44,099,433 View the variant detail on this assembly version.
hg38 chr2:43,872,294-43,872,294

HGVS

Type Transcript Protein
RefSeq NM_022437.2:c.1199C>A NP_071882.1:p.Thr400Lys
Ensemble ENST00000272286.4:c.1199C>A ENST00000272286.4:p.Thr400Lys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.123
ToMMo:0.113
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.112

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605460 OMIM
HGNC 13887 HGNC
Ensembl ENSG00000143921 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6683192 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2023-04-04 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-14 criteria provided, multiple submitters, no conflicts Sitosterolemia 1 germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2018-12-03 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Cholesterol gallstones Studies have identified single nucleotide polymorphisms (SNP) D19H and T400K in ... BeFree 20594224 Detail
0.132 cholelithiasis To investigate a possible association between transporter gene polymorphism and ... BeFree 17612515 Detail
0.026 Hypercholesterolemia Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... BeFree 18522623 Detail
0.149 cholelithiasis Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... BeFree 18522623 Detail
0.131 cholecystolithiasis Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... BeFree 18522623 Detail
0.144 cholecystolithiasis Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... BeFree 18522623 Detail
0.131 cholecystolithiasis To investigate a possible association between transporter gene polymorphism and ... BeFree 17612515 Detail
0.144 cholecystolithiasis To investigate a possible association between transporter gene polymorphism and ... BeFree 17612515 Detail
<0.001 Malignant neoplasm of gallbladder Carriers of the ABCG8 haplotype C-C (rs4148217-rs11887534) had a 4.16-fold (95% ... BeFree 21062971 Detail
0.149 cholelithiasis These findings indicate that the T400K polymorphism in ABCG8 may be associated w... BeFree 17612515 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_022437.3(ABCG8):c.1199C>A (p.Thr400Lys) AND not specified ClinVar Detail
NM_022437.3(ABCG8):c.1199C>A (p.Thr400Lys) AND Sitosterolemia 1 ClinVar Detail
NM_022437.3(ABCG8):c.1199C>A (p.Thr400Lys) AND not provided ClinVar Detail
NM_022437.3(ABCG8):c.1199C>A (p.Thr400Lys) AND Cardiovascular phenotype ClinVar Detail
Studies have identified single nucleotide polymorphisms (SNP) D19H and T400K in the cholesterol tran... DisGeNET Detail
To investigate a possible association between transporter gene polymorphism and gallstone formation,... DisGeNET Detail
Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... DisGeNET Detail
Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... DisGeNET Detail
Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... DisGeNET Detail
Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... DisGeNET Detail
To investigate a possible association between transporter gene polymorphism and gallstone formation,... DisGeNET Detail
To investigate a possible association between transporter gene polymorphism and gallstone formation,... DisGeNET Detail
Carriers of the ABCG8 haplotype C-C (rs4148217-rs11887534) had a 4.16-fold (95% CI 1.71-10.1) risk o... DisGeNET Detail
These findings indicate that the T400K polymorphism in ABCG8 may be associated with the incidence of... 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
rs4148217 dbSNP
Genome
hg38
Position
chr2:43,872,294-43,872,294
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
114.46
Standard deviation of sample read depth (HGVD)
55.32
Number of reference allele (HGVD)
2119
Number of alternative allele (HGVD)
297
Allele Frequency (HGVD)
0.12293046357615894
Gene Symbol (HGVD)
ABCG8
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))
rs4148217
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1135
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1903
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8180
East Asian Allele Counts (ExAC)
915
East Asian Heterozygous Counts (ExAC)
821
East Asian Homozygous Counts (ExAC)
47
East Asian Allele Frequency (ExAC)
0.11185819070904646
Chromosome Counts in All Race (ExAC)
116184
Allele Counts in All Race (ExAC)
24936
Heterozygous Counts in All Race (ExAC)
19415
Homozygous Counts in All Race (ExAC)
2760
Allele Frequency in All Race (ExAC)
0.21462507746333404
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