rs104893629
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PP3_ModeratePP5_Very_Strong
The NM_000104.4(CYP1B1):c.1267A>T(p.Asn423Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
CYP1B1
NM_000104.4 missense
NM_000104.4 missense
Scores
8
7
1
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
CYP1B1 (HGNC:2597): (cytochrome P450 family 1 subfamily B member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. The enzyme encoded by this gene localizes to the endoplasmic reticulum and metabolizes procarcinogens such as polycyclic aromatic hydrocarbons and 17beta-estradiol. Mutations in this gene have been associated with primary congenital glaucoma; therefore it is thought that the enzyme also metabolizes a signaling molecule involved in eye development, possibly a steroid. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.923
PP5
Variant 2-38071087-T-A is Pathogenic according to our data. Variant chr2-38071087-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 7743.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-38071087-T-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP1B1 | NM_000104.4 | c.1267A>T | p.Asn423Tyr | missense_variant | 3/3 | ENST00000610745.5 | NP_000095.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP1B1 | ENST00000610745.5 | c.1267A>T | p.Asn423Tyr | missense_variant | 3/3 | 1 | NM_000104.4 | ENSP00000478561.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251282Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135828
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GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460454Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 726256
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Glaucoma 3A Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2004 | - - |
Glaucoma, primary open angle, juvenile-onset Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2004 | - - |
Primary congenital glaucoma Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 28, 2023 | Variant summary: CYP1B1 c.1267A>T (p.Asn423Tyr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251282 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1267A>T has been reported in the literature in at least three compound heterozygous individuals affected with Primary Congenital Glaucoma and was shown to segregate with disease in two siblings (Colomb_2003, Melki_2004, Voltzke_2019 [No PubMed ID]). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 14635112, 15342693). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
Congenital glaucoma Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 20, 2023 | In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CYP1B1 protein function. ClinVar contains an entry for this variant (Variation ID: 7743). This missense change has been observed in individual(s) with CYP1B1-related glaucoma and/or primary congenital glaucoma (PMID: 14635112, 15342693). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs104893629, gnomAD 0.003%). This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 423 of the CYP1B1 protein (p.Asn423Tyr). - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D;T;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H;.;H
PrimateAI
Uncertain
T
Sift4G
Pathogenic
D;D;D
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at