ClinVar Genomic variation as it relates to human health
NM_000104.4(CYP1B1):c.1169G>A (p.Arg390His)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000104.4(CYP1B1):c.1169G>A (p.Arg390His)
Variation ID: 592512 Accession: VCV000592512.26
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p22.2 2: 38071185 (GRCh38) [ NCBI UCSC ] 2: 38298328 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 16, 2018 Oct 8, 2024 Mar 26, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000104.4:c.1169G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000095.2:p.Arg390His missense NC_000002.12:g.38071185C>T NC_000002.11:g.38298328C>T NG_008386.2:g.9917G>A - Protein change
- R390H
- Other names
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p.Arg390His
- Canonical SPDI
- NC_000002.12:38071184:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD) 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00009
Exome Aggregation Consortium (ExAC) 0.00015
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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CYP1B1 | - | - |
GRCh38 GRCh37 |
463 | 549 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Jul 26, 2022 | RCV000727642.13 | |
Pathogenic/Likely pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Mar 26, 2024 | RCV002272338.8 | |
Pathogenic (2) |
criteria provided, single submitter
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May 20, 2023 | RCV003448341.6 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 29, 2024 | RCV003987680.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 31, 2024 | RCV003758916.2 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Aug 03, 2018)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000854928.1
First in ClinVar: Dec 16, 2018 Last updated: Dec 16, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Likely pathogenic
(May 03, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: no
Allele origin:
unknown
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Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV001251756.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
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Pathogenic
(Sep 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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Anterior segment dysgenesis 6
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002556610.2
First in ClinVar: Aug 08, 2022 Last updated: Dec 17, 2022 |
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Pathogenic
(Jul 26, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001811030.3
First in ClinVar: Sep 08, 2021 Last updated: Mar 04, 2023 |
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 30820150, 25527694, … (more)
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 30820150, 25527694, 27508083, 19536304, 31236345, 29903728, 22878448, 19204079, 30108387, 30270463, 29540704, 34019190, 32830442, 19247456, 9497261, 25018621, 15475877) (less)
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Pathogenic
(Aug 31, 2023)
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criteria provided, single submitter
Method: clinical testing
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Anterior segment dysgenesis 6
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
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Pediatrics Genetics, Post Graduate Institute of Medical Education and Research
Accession: SCV004031059.1
First in ClinVar: Sep 03, 2023 Last updated: Sep 03, 2023 |
Comment:
This variant is not present in gnomad. PM1+PM2+PP3+PP5
Indication for testing: Neonatal-Onset Congenital Ectropion Uveae
Age: 0-9 years
Sex: female
Ethnicity/Population group: North Indian
Geographic origin: India
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Likely pathogenic
(Nov 16, 2023)
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criteria provided, single submitter
Method: clinical testing
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Anterior segment dysgenesis 6
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV004123120.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
A homozygous missense variant in exon 3 of the CYP1B1 gene that results in the amino acid substitution of Histidine for Arginine at codon 390 … (more)
A homozygous missense variant in exon 3 of the CYP1B1 gene that results in the amino acid substitution of Histidine for Arginine at codon 390 (p.Arg390His) was detected. The observed variant has previously been reported in patients affected with congenital glaucoma [PMID: 9497261]. This variant has not been reported in the 1000 genomes databases and has a minor allele frequency of 0.006%, 0.009% and 0.004% in the gnomAD (v3.1), gnomdAD (v2.1) and topmed databases respectively. The in-silico prediction of the variant are probably damaging by PolyPhen-2 (HumDiv), damaging by SIFT and LRT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as likely pathogenic. (less)
Clinical Features:
Vitiligo (present)
Age: 10-19 years
Sex: male
Method: DNA was used to perform targeted gene capture using a custom capture kit. Libraries were sequenced to mean >80-100X coverage on the Illumina sequencing platform. Sequence obtained were aligned to human references genome using BWA program and analyzed using Picard and GATK-Lite toolkit to identify variants in the targeted genes relevant to clinical indication.
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Pathogenic
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Congenital glaucoma
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004460649.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 390 of the CYP1B1 protein (p.Arg390His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 390 of the CYP1B1 protein (p.Arg390His). This variant is present in population databases (rs56010818, gnomAD 0.06%). This missense change has been observed in individual(s) with primary congenital glaucoma (PMID: 19536304, 27508083, 30108387). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 592512). 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 with a positive predictive value of 80%. This variant disrupts the p.Arg390 amino acid residue in CYP1B1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15037581, 20664688; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jan 29, 2024)
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criteria provided, single submitter
Method: clinical testing
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Primary congenital glaucoma
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004803933.1
First in ClinVar: Mar 30, 2024 Last updated: Mar 30, 2024 |
Comment:
Variant summary: CYP1B1 c.1169G>A (p.Arg390His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging … (more)
Variant summary: CYP1B1 c.1169G>A (p.Arg390His) 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 9.2e-05 in 249616 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in CYP1B1 causing Primary Congenital Glaucoma (9.2e-05 vs 0.0043), allowing no conclusion about variant significance. c.1169G>A has been reported in the literature as a biallelic genotype in many individuals affected with Primary Congenital Glaucoma and has been found to segregate with disease in multiple families (e.g. Sheikh_2014, Chitsazian_2007). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 17591938, 25018621). ClinVar contains an entry for this variant (Variation ID: 592512). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Anterior segment dysgenesis 6
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV005042563.1
First in ClinVar: May 12, 2024 Last updated: May 12, 2024 |
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Pathogenic
(Mar 26, 2024)
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criteria provided, single submitter
Method: clinical testing
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Anterior segment dysgenesis 6
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004215458.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(May 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Glaucoma 3A
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004176447.4
First in ClinVar: Dec 17, 2023 Last updated: Oct 08, 2024 |
Comment:
The observed missense c.1169G>A(p.Arg390His) variant in CYP1B1 gene has been reported in homozygous or compound heterozygous state in individuals affected with primary congenital glaucoma (Rauf … (more)
The observed missense c.1169G>A(p.Arg390His) variant in CYP1B1 gene has been reported in homozygous or compound heterozygous state in individuals affected with primary congenital glaucoma (Rauf B, et. al., 2016; Su CC, et. al., 2012). This variant is present with an allele frequency of 0.009% in gnomAD Exomes database. This variant has been submitted to the ClinVar database as Likely pathogenic/Pathogenic (multiple submissions). Multiple lines of computational evidence ( SIFT - damaging and MutationTaster - disease causing) predict a damaging effect on protein structure and function for this variant. The amino acid change p.Arg390His in CYP1B1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 390 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. (less)
Clinical Features:
Abnormality of the eye (present)
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Pathogenic
(Dec 06, 2023)
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no assertion criteria provided
Method: research
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Glaucoma 3A
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Basic Medical Sciences, Khyber Medical University, Peshawar
Accession: SCV005088698.1
First in ClinVar: Aug 18, 2024 Last updated: Aug 18, 2024 |
Comment:
This variant is classified as pathogenic and its already reported. The pubmed link for this article via PMID is 9497261
Age: 0-9 years
Ethnicity/Population group: Pakhtun
Geographic origin: Pakistan
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Neonatal-Onset Congenital Ectropion Uveae May Be Caused by a Distinct CYP1B1 Pathologic Variant. | Kaushik S | American journal of ophthalmology | 2022 | PMID: 35085548 |
Clinical variability of CYP1B1 gene variants in Pakistani primary congenital glaucoma families. | Bashir R | JPMA. The Journal of the Pakistan Medical Association | 2018 | PMID: 30108387 |
A spectrum of CYP1B1 mutations associated with primary congenital glaucoma in families of Pakistani descent. | Rauf B | Human genome variation | 2016 | PMID: 27508083 |
Mutation spectrum of CYP1B1 in Chinese patients with primary open-angle glaucoma. | Gong B | The British journal of ophthalmology | 2015 | PMID: 25527694 |
Mutational spectrum of the CYP1B1 gene in Pakistani patients with primary congenital glaucoma: novel variants and genotype-phenotype correlations. | Sheikh SA | Molecular vision | 2014 | PMID: 25018621 |
Mutations in the CYP1B1 gene may contribute to juvenile-onset open-angle glaucoma. | Su CC | Eye (London, England) | 2012 | PMID: 22878448 |
Screening of CYP1B1 and MYOC in Moroccan families with primary congenital glaucoma: three novel mutations in CYP1B1. | Hilal L | Molecular vision | 2010 | PMID: 20664688 |
Mutation spectrum of CYP1B1 in North Indian congenital glaucoma patients. | Tanwar M | Molecular vision | 2009 | PMID: 19536304 |
CYP1B1 mutation profile of Iranian primary congenital glaucoma patients and associated haplotypes. | Chitsazian F | The Journal of molecular diagnostics : JMD | 2007 | PMID: 17591938 |
Correlations of genotype with phenotype in Indian patients with primary congenital glaucoma. | Panicker SG | Investigative ophthalmology & visual science | 2004 | PMID: 15037581 |
Sequence analysis and homology modeling suggest that primary congenital glaucoma on 2p21 results from mutations disrupting either the hinge region or the conserved core structures of cytochrome P4501B1. | Stoilov I | American journal of human genetics | 1998 | PMID: 9497261 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP1B1 | - | - | - | - |
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Text-mined citations for rs56010818 ...
HelpRecord last updated Oct 08, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.