chr2:38298139:T>C Detail (hg19) (CYP1B1, LOC128772254)

Information

Genome

Assembly Position
hg19 chr2:38,298,139-38,298,139
hg38 chr2:38,070,996-38,070,996 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000104.3:c.1358A>G NP_000095.2:p.Asn453Ser
Ensemble ENST00000490576.2:c.1358A>G ENST00000490576.2:p.Asn453Ser
ENST00000494864.1:c.245A>G ENST00000494864.1:p.Asn82Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.004

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 tgv6523881 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 Likely benign 2021-07-30 criteria provided, multiple submitters, no conflicts Glaucoma 3A germline Detail
Benign Likely benign 2016-10-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2024-02-01 criteria provided, single submitter Congenital glaucoma germline Detail
Benign 2021-07-30 criteria provided, single submitter anterior segment dysgenesis 6 germline Detail
Likely benign 2022-05-12 criteria provided, single submitter Glaucoma 3, primary infantile, B,Glaucoma 3A,anterior segment dysgenesis 6 unknown Detail
Likely benign 2022-05-12 criteria provided, single submitter Glaucoma 3, primary infantile, B,Glaucoma 3A,anterior segment dysgenesis 6 unknown Detail
Likely benign 2022-05-12 criteria provided, single submitter Glaucoma 3, primary infantile, B,Glaucoma 3A,anterior segment dysgenesis 6 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.006 prostate carcinoma According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and... BeFree 24682418 Detail
0.005 prostate carcinoma According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and... BeFree 24682418 Detail
0.041 Malignant neoplasm of prostate According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and... BeFree 24682418 Detail
0.021 Malignant neoplasm of prostate According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and... BeFree 24682418 Detail
0.017 endometrial carcinoma The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymor... BeFree 20381444 Detail
0.017 breast carcinoma We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (he... BeFree 22418777 Detail
0.001 endometrial carcinoma The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymor... BeFree 20381444 Detail
0.097 Malignant neoplasm of breast We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (he... BeFree 22418777 Detail
0.017 breast carcinoma We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (he... BeFree 22418777 Detail
<0.001 Malignant neoplasm of endometrium The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymor... BeFree 20381444 Detail
0.003 Malignant neoplasm of endometrium The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymor... BeFree 20381444 Detail
0.008 Mammographic Density [After multivariate adjustment, the CYP1B1 rs162555 CC genotype was associated w... GAD 19630952 Detail
0.097 Malignant neoplasm of breast We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (he... BeFree 22418777 Detail
0.003 colorectal carcinoma Carriers of variant Ser allele in codon 453 of cytochrome P450 1B1 (rs1800440) w... BeFree 20878130 Detail
0.030 colorectal cancer Carriers of variant Ser allele in codon 453 of cytochrome P450 1B1 (rs1800440) w... BeFree 20878130 Detail
0.001 uterine corpus cancer The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymor... BeFree 20381444 Detail
0.003 uterine corpus cancer The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymor... BeFree 20381444 Detail
<0.001 Gastrointestinal Stromal Tumors Although none of the association p-values were statistically significant after a... BeFree 23637977 Detail
0.760 Gastrointestinal Stromal Tumors Although none of the association p-values were statistically significant after a... BeFree 23637977 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND not specified ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND Glaucoma 3A ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND not provided ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND Congenital glaucoma ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND Anterior segment dysgenesis 6 ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND multiple conditions ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND multiple conditions ClinVar Detail
NM_000104.4(CYP1B1):c.1358A>G (p.Asn453Ser) AND multiple conditions ClinVar Detail
According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and SULT2B1 (rs12460535... DisGeNET Detail
According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and SULT2B1 (rs12460535... DisGeNET Detail
According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and SULT2B1 (rs12460535... DisGeNET Detail
According to a multivariate analysis, CYP1B1 (rs1800440), COMT (rs16982844), and SULT2B1 (rs12460535... DisGeNET Detail
The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associate... DisGeNET Detail
We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (het) = 0.003) and with... DisGeNET Detail
The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associate... DisGeNET Detail
We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (het) = 0.003) and with... DisGeNET Detail
We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (het) = 0.003) and with... DisGeNET Detail
The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associate... DisGeNET Detail
The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associate... DisGeNET Detail
[After multivariate adjustment, the CYP1B1 rs162555 CC genotype was associated with a 9.4% higher ma... DisGeNET Detail
We detected SNP-HT interactions in women overall within CYP1B1 (rs1800440; p (het) = 0.003) and with... DisGeNET Detail
Carriers of variant Ser allele in codon 453 of cytochrome P450 1B1 (rs1800440) were at a significant... DisGeNET Detail
Carriers of variant Ser allele in codon 453 of cytochrome P450 1B1 (rs1800440) were at a significant... DisGeNET Detail
The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associate... DisGeNET Detail
The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associate... DisGeNET Detail
Although none of the association p-values were statistically significant after adjustment for multip... DisGeNET Detail
Although none of the association p-values were statistically significant after adjustment for multip... 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
rs1800440 dbSNP
Genome
hg19
Position
chr2:38,298,139-38,298,139
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
146.62
Standard deviation of sample read depth (HGVD)
67.30
Number of reference allele (HGVD)
2415
Number of alternative allele (HGVD)
5
Allele Frequency (HGVD)
0.002066115702479339
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))
rs1800440
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0018
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
31
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)
33
East Asian Heterozygous Counts (ExAC)
33
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.003813265541945921
Chromosome Counts in All Race (ExAC)
121388
Allele Counts in All Race (ExAC)
18782
Heterozygous Counts in All Race (ExAC)
15216
Homozygous Counts in All Race (ExAC)
1783
Allele Frequency in All Race (ExAC)
0.15472699113586186
Genome browser