chr2:234681059:T>G Detail (hg19) (UGT1A, UGT1A10, UGT1A8, UGT1A7, UGT1A6, UGT1A5, UGT1A9, UGT1A4, UGT1A1, UGT1A3)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:234,681,059-234,681,059 |
| hg38 | chr2:233,772,413-233,772,413 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000463.2:c.1456T>G | NP_000454.1:p.Tyr486Asp |
| Ensemble | ENST00000305208.10:c.1456T>G | ENST00000305208.10:p.Tyr486Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019075.2:c.1447T>G | NP_061948.1:p.Tyr483Asp |
| Ensemble | ENST00000344644.10:c.1447T>G | ENST00000344644.10:p.Tyr483Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019093.2:c.1459T>G | NP_061966.1:p.Tyr487Asp |
| Ensemble | ENST00000482026.6:c.1459T>G | ENST00000482026.6:p.Tyr487Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_007120.2:c.1459T>G | NP_009051.1:p.Tyr487Asp |
| Ensemble | ENST00000373409.8:c.1459T>G | ENST00000373409.8:p.Tyr487Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019078.1:c.1459T>G | NP_061951.1:p.Tyr487Asp |
| Ensemble | ENST00000373414.4:c.1459T>G | ENST00000373414.4:p.Tyr487Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_205862.1:c.652T>G | NP_995584.1:p.Tyr218Asp |
| NM_001072.3:c.1453T>G | NP_001063.2:p.Tyr485Asp | |
| Ensemble | ENST00000373424.5:c.652T>G | ENST00000373424.5:p.Tyr218Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019077.2:c.1447T>G | NP_061950.2:p.Tyr483Asp |
| Ensemble | ENST00000373426.4:c.1447T>G | ENST00000373426.4:p.Tyr483Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019076.4:c.1447T>G | NP_061949.3:p.Tyr483Asp |
| Ensemble | ENST00000373450.5:c.1447T>G | ENST00000373450.5:p.Tyr483Asp |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_021027.2:c.1447T>G | NP_066307.1:p.Tyr483Asp |
| Ensemble | ENST00000354728.5:c.1447T>G | ENST00000354728.5:p.Tyr483Asp |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 8 |
| 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:0.001 |
Prediction
ClinVar
| Clinical Significance |
Pathogenic
Likely pathogenic
|
| Review star |  |
| Show details | |
Links
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 191740 | OMIM |
| HGNC | 12530 | HGNC | |
| Ensembl | ENSG00000241635 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606435 | OMIM |
| HGNC | 12531 | HGNC | |
| Ensembl | ENSG00000242515 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606428 | OMIM |
| HGNC | 12535 | HGNC | |
| Ensembl | ENSG00000288702 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606429 | OMIM |
| HGNC | 12536 | HGNC | |
| Ensembl | ENSG00000244474 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606430 | OMIM |
| HGNC | 12537 | HGNC | |
| Ensembl | ENSG00000288705 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606431 | OMIM |
| HGNC | 12538 | HGNC | |
| Ensembl | ENSG00000167165 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
| Type | Database | ID | Link |
|---|---|---|---|
| Gene | MIM | 606432 | OMIM |
| HGNC | 12539 | HGNC | |
| Ensembl | ENSG00000244122 | Ensembl | |
| NCBI | NCBI | ||
| Gene Cards | Gene Cards | ||
| OncoKB | OncoKB |
| Type | Database | ID | Link |
|---|---|---|---|
| Variant | TogoVar | tgv10921398 | TogoVar |
| COSMIC | |||
| MONDO |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
|
2007-12-01 | no assertion criteria provided | Lucey-Driscoll syndrome |
germline
|
Detail |
|
Pathogenic
Likely pathogenic
|
2022-01-03 | criteria provided, multiple submitters, no conflicts | Crigler-Najjar syndrome, type II |
germline
|
Detail |
|
Pathogenic
|
2014-04-10 | criteria provided, single submitter |
germline
|
Detail | |
|
Likely pathogenic
|
2018-10-31 | criteria provided, single submitter | Bilirubin, serum level of, quantitative trait locus 1,Crigler-Najjar syndrome type 1,Crigler-Najjar syndrome, type II,Gilbert syndrome,Lucey-Driscoll syndrome |
unknown
|
Detail |
|
Likely pathogenic
|
2018-10-31 | criteria provided, single submitter | Bilirubin, serum level of, quantitative trait locus 1,Crigler-Najjar syndrome type 1,Crigler-Najjar syndrome, type II,Gilbert syndrome,Lucey-Driscoll syndrome |
unknown
|
Detail |
|
Likely pathogenic
|
2018-10-31 | criteria provided, single submitter | Bilirubin, serum level of, quantitative trait locus 1,Crigler-Najjar syndrome type 1,Crigler-Najjar syndrome, type II,Gilbert syndrome,Lucey-Driscoll syndrome |
unknown
|
Detail |
|
Likely pathogenic
|
2018-10-31 | criteria provided, single submitter | Bilirubin, serum level of, quantitative trait locus 1,Crigler-Najjar syndrome type 1,Crigler-Najjar syndrome, type II,Gilbert syndrome,Lucey-Driscoll syndrome |
unknown
|
Detail |
|
Likely pathogenic
|
2018-10-31 | criteria provided, single submitter | Bilirubin, serum level of, quantitative trait locus 1,Crigler-Najjar syndrome type 1,Crigler-Najjar syndrome, type II,Gilbert syndrome,Lucey-Driscoll syndrome |
unknown
|
Detail |
|
Pathogenic
|
2019-05-01 | no assertion criteria provided | Gilbert syndrome |
inherited
|
Detail |
|
Pathogenic
|
2023-12-07 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Pathogenic
|
2023-12-06 | criteria provided, single submitter | UGT1A1-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.483 | Crigler Najjar syndrome, type 2 | Sequence analysis of the UGT1A1 gene revealed that she was a compound heterozygo... | BeFree | 21319362 | Detail |
| 0.483 | Crigler Najjar syndrome, type 2 | UGT1A1 coding region mutations, including UGT1A1*6 (G71R), UGT1A1*7 (Y486D), UGT... | BeFree | 18004206 | Detail |
| 0.295 | Gilbert Disease (disorder) | UGT1A1 coding region mutations, including UGT1A1*6 (G71R), UGT1A1*7 (Y486D), UGT... | BeFree | 18004206 | Detail |
| 0.483 | Crigler Najjar syndrome, type 2 | Contribution of two missense mutations (G71R and Y486D) of the bilirubin UDP gly... | BeFree | 9630669 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND Lucey-Driscoll syndrome | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND Crigler-Najjar syndrome, type II | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND Hyperbilirubinemia | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND multiple conditions | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND multiple conditions | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND multiple conditions | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND multiple conditions | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND multiple conditions | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND Gilbert syndrome | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND not provided | ClinVar | Detail |
| NM_000463.3(UGT1A1):c.1456T>G (p.Tyr486Asp) AND UGT1A1-related disorder | ClinVar | Detail |
| Sequence analysis of the UGT1A1 gene revealed that she was a compound heterozygote with p.[G71R; Y48... | DisGeNET | Detail |
| UGT1A1 coding region mutations, including UGT1A1*6 (G71R), UGT1A1*7 (Y486D), UGT1A1*27 (P229Q) and U... | DisGeNET | Detail |
| UGT1A1 coding region mutations, including UGT1A1*6 (G71R), UGT1A1*7 (Y486D), UGT1A1*27 (P229Q) and U... | DisGeNET | Detail |
| Contribution of two missense mutations (G71R and Y486D) of the bilirubin UDP glycosyltransferase (UG... | 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
- rs34993780 dbSNP
- Genome
- hg19
- Position
- chr2:234,681,059-234,681,059
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 72.73
- Standard deviation of sample read depth (HGVD)
- 33.62
- Number of reference allele (HGVD)
- 2417
- Number of alternative allele (HGVD)
- 3
- Allele Frequency (HGVD)
- 0.0012396694214876034
- Gene Symbol (HGVD)
- UGT1A1
- 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))
- rs34993780
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0014
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 24
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 10
- East Asian Heterozygous Counts (ExAC)
- 10
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.0011555350127108851
- Chromosome Counts in All Race (ExAC)
- 121404
- Allele Counts in All Race (ExAC)
- 18
- Heterozygous Counts in All Race (ExAC)
- 18
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 1.4826529603637441E-4
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