chr2:38302177:C>A Detail (hg19) (CYP1B1)

Information

Genome

Assembly Position
hg19 chr2:38,302,177-38,302,177
hg38 chr2:38,075,034-38,075,034 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000104.3:c.355G>T NP_000095.2:p.Ala119Ser
Ensemble ENST00000490576.2:c.355G>T ENST00000490576.2:p.Ala119Ser
ENST00000494864.1:c.-70-3724G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.121
ToMMo:0.113
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.275

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601771 OMIM
HGNC 2597 HGNC
Ensembl ENSG00000138061 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6524234 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-12-03 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-30 criteria provided, multiple submitters, no conflicts Glaucoma 3A germline Detail
Benign 2024-02-01 criteria provided, single submitter Congenital glaucoma germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
Benign 2021-07-30 criteria provided, single submitter anterior segment dysgenesis 6 germline Detail
Benign 2022-04-28 criteria provided, single submitter Glaucoma 3A,anterior segment dysgenesis 6,Glaucoma 3, primary infantile, B unknown Detail
Benign 2022-04-28 criteria provided, single submitter Glaucoma 3A,anterior segment dysgenesis 6,Glaucoma 3, primary infantile, B unknown Detail
Benign 2022-04-28 criteria provided, single submitter Glaucoma 3A,anterior segment dysgenesis 6,Glaucoma 3, primary infantile, B unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 Uterine Fibroids The genetic polymorphism of rs3087869 (IVS1+2329C>T) (OR 3.200, 95% CI 1.614-... BeFree 24777039 Detail
0.107 Malignant neoplasm of urinary bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.093 Malignant neoplasm of urinary bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.011 Malignant neoplasm of urinary bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.027 Carcinoma of bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.002 Uterine Fibroids The genetic polymorphism of rs3087869 (IVS1+2329C>T) (OR 3.200, 95% CI 1.614-... BeFree 24777039 Detail
0.001 Uterine Fibroids The genetic polymorphisms of IVS1+2329C>T and Val158Met loci in COMT, Ile462V... BeFree 24320736 Detail
0.002 Uterine Fibroids The genetic polymorphisms of IVS1+2329C>T and Val158Met loci in COMT, Ile462V... BeFree 24320736 Detail
0.030 Malignant neoplasm of urinary bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.013 Carcinoma of bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.366 Glaucoma, Primary Open Angle Moreover, one haplotype consisting of rs1056827 and rs100012 in CYP1B1 gene was ... BeFree 23206929 Detail
0.004 Uterine Fibroids The genetic polymorphism of rs3087869 (IVS1+2329C>T) (OR 3.200, 95% CI 1.614-... BeFree 24777039 Detail
0.002 Carcinoma of bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.003 Carcinoma of bladder CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (n... BeFree 23886208 Detail
0.004 Uterine Fibroids The genetic polymorphisms of IVS1+2329C>T and Val158Met loci in COMT, Ile462V... BeFree 24320736 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND not specified ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND Glaucoma 3A ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND Congenital glaucoma ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND not provided ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND Anterior segment dysgenesis 6 ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND multiple conditions ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND multiple conditions ClinVar Detail
NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND multiple conditions ClinVar Detail
The genetic polymorphism of rs3087869 (IVS1+2329C>T) (OR 3.200, 95% CI 1.614-6.345) and rs4680 (V... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
The genetic polymorphism of rs3087869 (IVS1+2329C>T) (OR 3.200, 95% CI 1.614-6.345) and rs4680 (V... DisGeNET Detail
The genetic polymorphisms of IVS1+2329C>T and Val158Met loci in COMT, Ile462Val and Gly45Asp loci... DisGeNET Detail
The genetic polymorphisms of IVS1+2329C>T and Val158Met loci in COMT, Ile462Val and Gly45Asp loci... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
Moreover, one haplotype consisting of rs1056827 and rs100012 in CYP1B1 gene was significantly associ... DisGeNET Detail
The genetic polymorphism of rs3087869 (IVS1+2329C>T) (OR 3.200, 95% CI 1.614-6.345) and rs4680 (V... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
CYP1A1 (Ile462Val), CYP1B1 (Ala119Ser and Val432Leu), GSTM1 (null), and GSTT1 (null) polymorphisms a... DisGeNET Detail
The genetic polymorphisms of IVS1+2329C>T and Val158Met loci in COMT, Ile462Val and Gly45Asp loci... 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
rs1056827 dbSNP
Genome
hg19
Position
chr2:38,302,177-38,302,177
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1120
Mean of sample read depth (HGVD)
53.67
Standard deviation of sample read depth (HGVD)
23.84
Number of reference allele (HGVD)
1969
Number of alternative allele (HGVD)
271
Allele Frequency (HGVD)
0.12098214285714286
Gene Symbol (HGVD)
CYP1B1
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))
rs1056827
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1131
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1896
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
4820
East Asian Allele Counts (ExAC)
1325
East Asian Heterozygous Counts (ExAC)
1111
East Asian Homozygous Counts (ExAC)
107
East Asian Allele Frequency (ExAC)
0.274896265560166
Chromosome Counts in All Race (ExAC)
72358
Allele Counts in All Race (ExAC)
29809
Heterozygous Counts in All Race (ExAC)
19989
Homozygous Counts in All Race (ExAC)
4910
Allele Frequency in All Race (ExAC)
0.41196550485088035
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