chr2:43813262:G>C Detail (hg38) (DYNC2LI1, ABCG5)

Information

Genome

Assembly Position
hg19 chr2:44,040,401-44,040,401 View the variant detail on this assembly version.
hg38 chr2:43,813,262-43,813,262

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000405322.8:c.1810C>G ENST00000405322.8:p.Gln604Glu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.125
ToMMo:0.119
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.117

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605459 OMIM
HGNC 13886 HGNC
Ensembl ENSG00000138075 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6680586 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2024-01-31 criteria provided, multiple submitters, no conflicts sitosterolemia germline unknown Detail
Benign Likely benign 2023-04-04 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-03-06 criteria provided, single submitter Sitosterolemia 1 germline Detail
Benign 2018-07-05 criteria provided, single submitter 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
0.132 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
<0.001 Insulin resistance syndrome Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... BeFree 15175352 Detail
0.144 cholecystolithiasis Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABC... BeFree 18522623 Detail
0.132 cholelithiasis Recently, variants of the hepatocanalicular cholesterol hemitransporters ABCG5/8... BeFree 20497293 Detail
0.131 cholecystolithiasis To investigate a possible association between transporter gene polymorphism and ... BeFree 17612515 Detail
<0.001 Insulin resistance syndrome Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... BeFree 15175352 Detail
0.144 cholecystolithiasis To investigate a possible association between transporter gene polymorphism and ... BeFree 17612515 Detail
<0.001 Metabolic syndrome X Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... BeFree 15175352 Detail
0.003 Metabolic syndrome X Low serum cholesterol and cholesterol absorption were linked to the D19H polymor... BeFree 15175352 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_022436.3(ABCG5):c.1810C>G (p.Gln604Glu) AND Sitosterolemia ClinVar Detail
NM_022436.3(ABCG5):c.1810C>G (p.Gln604Glu) AND not specified ClinVar Detail
NM_022436.3(ABCG5):c.1810C>G (p.Gln604Glu) AND Sitosterolemia 1 ClinVar Detail
NM_022436.3(ABCG5):c.1810C>G (p.Gln604Glu) AND not provided ClinVar Detail
NM_022436.3(ABCG5):c.1810C>G (p.Gln604Glu) AND Cardiovascular phenotype ClinVar 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
Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... DisGeNET Detail
Various polymorphisms (A632V, T400K, D19H, M429V, and C54Y) in the ABCG8 and ABCG5 (Q604E) gene have... DisGeNET Detail
Recently, variants of the hepatocanalicular cholesterol hemitransporters ABCG5/8 were linked to gall... DisGeNET Detail
To investigate a possible association between transporter gene polymorphism and gallstone formation,... DisGeNET Detail
Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... DisGeNET Detail
To investigate a possible association between transporter gene polymorphism and gallstone formation,... DisGeNET Detail
Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... DisGeNET Detail
Low serum cholesterol and cholesterol absorption were linked to the D19H polymorphism of the ABCG8 g... 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
rs6720173 dbSNP
Genome
hg38
Position
chr2:43,813,262-43,813,262
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
84.63
Standard deviation of sample read depth (HGVD)
37.60
Number of reference allele (HGVD)
2118
Number of alternative allele (HGVD)
302
Allele Frequency (HGVD)
0.12479338842975207
Gene Symbol (HGVD)
ABCG5
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))
rs6720173
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1185
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1986
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8556
East Asian Allele Counts (ExAC)
1003
East Asian Heterozygous Counts (ExAC)
889
East Asian Homozygous Counts (ExAC)
57
East Asian Allele Frequency (ExAC)
0.11722767648433847
Chromosome Counts in All Race (ExAC)
118454
Allele Counts in All Race (ExAC)
24837
Heterozygous Counts in All Race (ExAC)
19133
Homozygous Counts in All Race (ExAC)
2852
Allele Frequency in All Race (ExAC)
0.20967633005217215
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