ClinVar Genomic variation as it relates to human health
NM_001395413.1(POR):c.1361G>A (p.Arg454His)
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_001395413.1(POR):c.1361G>A (p.Arg454His)
Variation ID: 16907 Accession: VCV000016907.14
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7q11.23 7: 75985179 (GRCh38) [ NCBI UCSC ] 7: 75614497 (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 May 9, 2015 Feb 14, 2024 Jan 31, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001395413.1:c.1361G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001382342.1:p.Arg454His missense NM_001367562.3:c.1361G>A NP_001354491.2:p.Arg454His missense NM_001382655.3:c.1415G>A NP_001369584.2:p.Arg472His missense NM_001382657.2:c.1361G>A NP_001369586.2:p.Arg454His missense NM_001382658.3:c.1361G>A NP_001369587.2:p.Arg454His missense NM_001382659.3:c.1361G>A NP_001369588.2:p.Arg454His missense NM_001382662.3:c.1239+221G>A intron variant NC_000007.14:g.75985179G>A NC_000007.13:g.75614497G>A NG_008930.1:g.75078G>A - Protein change
- R454H, R472H
- Other names
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R457H
- Canonical SPDI
- NC_000007.14:75985178:G:A
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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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0.00020 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00005
Exome Aggregation Consortium (ExAC) 0.00008
1000 Genomes Project 30x 0.00016
1000 Genomes Project 0.00020
- 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
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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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POR | - | - |
GRCh38 GRCh37 |
720 | 862 |
Conditions - Germline
Condition
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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 (1) |
no assertion criteria provided
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Mar 15, 2006 | RCV000018406.36 | |
Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Jan 31, 2024 | RCV000018407.47 | |
Pathogenic (1) |
criteria provided, single submitter
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May 16, 2022 | RCV002490385.8 | |
Pathogenic (2) |
criteria provided, single submitter
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Jul 17, 2023 | RCV003150931.10 |
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
(May 16, 2022)
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criteria provided, single submitter
Method: clinical testing
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Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis
Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002789467.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Jul 17, 2023)
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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: SCV004014196.1
First in ClinVar: Jul 22, 2023 Last updated: Jul 22, 2023 |
Comment:
Published functional studies demonstrate a damaging effect resulting in reduced enzyme activity (Flck et al., 2004); In silico analysis supports that this missense variant has … (more)
Published functional studies demonstrate a damaging effect resulting in reduced enzyme activity (Flck et al., 2004); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21741353, 20732302, 20940534, 20124576, 20697309, 32820517, 16495354, 17062779, 22252407, 22123124, 17635179, 22162478, 18551037, 22547083, 21808038, 16470797, 28288674, 16439592, 18853185, 28841001, 29289577, 31299979, 31754721, 33336784, 29944250, 32973886, 35070845, 19258400, 14758361) (less)
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Pathogenic
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000828629.4
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 457 of the POR protein (p.Arg457His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 457 of the POR protein (p.Arg457His). This variant is present in population databases (rs28931608, gnomAD 0.05%). This missense change has been observed in individuals with POR-related conditions (PMID: 14758361, 15483095, 20124576, 28841001). ClinVar contains an entry for this variant (Variation ID: 16907). 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 POR protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects POR function (PMID: 18551037, 20940534, 22252407, 22547083). For these reasons, this variant has been classified as Pathogenic. (less)
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Likely pathogenic
(Mar 18, 2016)
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criteria provided, single submitter
Method: reference population
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Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency
Affected status: unknown
Allele origin:
germline
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Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center
Accession: SCV000267459.1
First in ClinVar: Oct 11, 2015 Last updated: Oct 11, 2015 |
Number of individuals with the variant: 1
Age: 40-69 years
Ethnicity/Population group: East Asian
Geographic origin: South Korean
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Pathogenic
(Mar 15, 2006)
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no assertion criteria provided
Method: literature only
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ANTLEY-BIXLER SYNDROME WITH GENITAL ANOMALIES AND DISORDERED STEROIDOGENESIS
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000038688.3
First in ClinVar: Apr 04, 2013 Last updated: May 09, 2015 |
Comment on evidence:
In a child with Antley-Bixler syndrome and disordered steroidogenesis (ABS1; 201750), Fluck et al. (2004) found compound heterozygosity for a 1370G-A transition in the POR … (more)
In a child with Antley-Bixler syndrome and disordered steroidogenesis (ABS1; 201750), Fluck et al. (2004) found compound heterozygosity for a 1370G-A transition in the POR gene leading to an arg457-to-his (R457H) substitution on the maternal allele, and a 731+1G-A change (124015.0006) in the first base of the splice donor site of intron 6 on the paternal allele. The corresponding minigene construct retained intron 6, leading to a premature stop codon. In a female (46,XX) offspring of healthy, unrelated parents of Polish descent with congenital adrenal hyperplasia due to apparent combined deficiency of P450C17 and P450C21 (613571), Arlt et al. (2004) described compound heterozygosity for 2 mutations in the POR gene: A287P (124015.0002) and the R457H mutation. (Arlt et al. (2004) numbered these mutations A284P and R454H, respectively, according to the amino acid position in the protein (GenBank P16435).) The girl was born with clubfeet and ambiguous genitalia, including enlargement of the clitoris and partial labial fusion. Virilization did not progress after birth. Follow-up at 13 years of age showed a marfanoid habitus, scoliosis, arachnodactyly, dysplastic ears, and long, slim limbs. Ovarectomy due to rupture of large ovarian cysts was performed at 14 and 16 years of age. In this family, 5 preceding and 2 subsequent pregnancies resulted in early miscarriages. The unaffected father was heterozygous for A287P; the unaffected mother and younger brother were heterozygous for R457H. Huang et al. (2005) sequenced the POR gene in 29 individuals with a diagnosis of Antley-Bixler syndrome and/or hormonal findings that suggested POR deficiency. Fifteen patients carried POR mutations on both alleles, and 4 carried mutations on only 1 allele. The 34 affected POR alleles included 7 with R457H, in 4 Japanese, 1 African, and 2 white patients. Fukami et al. (2005) identified the R457H mutation in 10 of 16 alleles from 8 Japanese families with skeletal findings of ABS and abnormal genitalia and/or impaired steroidogenesis. R457H was associated with a specific haplotype; Fukami et al. (2005) suggested that the high frequency of R457H in the Japanese is due to a founder effect. Adachi et al. (2006) performed SNP analysis in 5 previously reported patients with POR deficiency and the R457H mutation (4 Japanese and 1 Polish), and found that the non-Japanese patient had the same SNP pattern as Japanese patients, suggesting that R457H is a global founder mutation. (less)
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Pathogenic
(Mar 15, 2006)
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no assertion criteria provided
Method: literature only
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DISORDERED STEROIDOGENESIS DUE TO CYTOCHROME P450 OXIDOREDUCTASE DEFICIENCY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000038689.3
First in ClinVar: Apr 04, 2013 Last updated: May 09, 2015 |
Comment on evidence:
In a child with Antley-Bixler syndrome and disordered steroidogenesis (ABS1; 201750), Fluck et al. (2004) found compound heterozygosity for a 1370G-A transition in the POR … (more)
In a child with Antley-Bixler syndrome and disordered steroidogenesis (ABS1; 201750), Fluck et al. (2004) found compound heterozygosity for a 1370G-A transition in the POR gene leading to an arg457-to-his (R457H) substitution on the maternal allele, and a 731+1G-A change (124015.0006) in the first base of the splice donor site of intron 6 on the paternal allele. The corresponding minigene construct retained intron 6, leading to a premature stop codon. In a female (46,XX) offspring of healthy, unrelated parents of Polish descent with congenital adrenal hyperplasia due to apparent combined deficiency of P450C17 and P450C21 (613571), Arlt et al. (2004) described compound heterozygosity for 2 mutations in the POR gene: A287P (124015.0002) and the R457H mutation. (Arlt et al. (2004) numbered these mutations A284P and R454H, respectively, according to the amino acid position in the protein (GenBank P16435).) The girl was born with clubfeet and ambiguous genitalia, including enlargement of the clitoris and partial labial fusion. Virilization did not progress after birth. Follow-up at 13 years of age showed a marfanoid habitus, scoliosis, arachnodactyly, dysplastic ears, and long, slim limbs. Ovarectomy due to rupture of large ovarian cysts was performed at 14 and 16 years of age. In this family, 5 preceding and 2 subsequent pregnancies resulted in early miscarriages. The unaffected father was heterozygous for A287P; the unaffected mother and younger brother were heterozygous for R457H. Huang et al. (2005) sequenced the POR gene in 29 individuals with a diagnosis of Antley-Bixler syndrome and/or hormonal findings that suggested POR deficiency. Fifteen patients carried POR mutations on both alleles, and 4 carried mutations on only 1 allele. The 34 affected POR alleles included 7 with R457H, in 4 Japanese, 1 African, and 2 white patients. Fukami et al. (2005) identified the R457H mutation in 10 of 16 alleles from 8 Japanese families with skeletal findings of ABS and abnormal genitalia and/or impaired steroidogenesis. R457H was associated with a specific haplotype; Fukami et al. (2005) suggested that the high frequency of R457H in the Japanese is due to a founder effect. Adachi et al. (2006) performed SNP analysis in 5 previously reported patients with POR deficiency and the R457H mutation (4 Japanese and 1 Polish), and found that the non-Japanese patient had the same SNP pattern as Japanese patients, suggesting that R457H is a global founder mutation. (less)
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Pathogenic
(Aug 15, 2022)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV003839908.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
This sequence change, c.1370G>A, is in exon 12 results and in an amino acid change, p.Arg457His. The p.Arg457His change affects a highly conserved amino acid … (more)
This sequence change, c.1370G>A, is in exon 12 results and in an amino acid change, p.Arg457His. The p.Arg457His change affects a highly conserved amino acid residue located in a domain of the POR protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, Align GVGD, REVEL) provide contradictory results for the p.Arg457His substitution. This sequence change has previously been described in several patients with cytochrome P450 oxidoreductase deficiency (POR) deficiency with or without Antley-Bixler syndrome and is considered a founder mutation in the Japanese population (PMID: 15483095, 16470797, 14758361, 19258400). This sequence change has been described in the gnomAD database with a frequency of 0.05% in the East Asian subpopulation (dbSNP rs28931608). These collective evidences indicate that this sequence change is pathogenic. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV002011802.2
First in ClinVar: Nov 06, 2021 Last updated: Oct 01, 2022 |
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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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A Case of Antley-Bixler Syndrome With a Novel Likely Pathogenic Variant (c.529G>C) in the POR Gene. | Oh J | Annals of laboratory medicine | 2017 | PMID: 28841001 |
Cytochrome P450 Oxidoreductase Deficiency. | Adam MP | - | 2017 | PMID: 20301592 |
Effect of P450 oxidoreductase variants on the metabolism of model substrates mediated by CYP2C9.1, CYP2C9.2, and CYP2C9.3. | Subramanian M | Pharmacogenetics and genomics | 2012 | PMID: 22547083 |
Altered human CYP3A4 activity caused by Antley-Bixler syndrome-related variants of NADPH-cytochrome P450 oxidoreductase measured in a robust in vitro system. | Moutinho D | Drug metabolism and disposition: the biological fate of chemicals | 2012 | PMID: 22252407 |
Effects of genetic variants of human P450 oxidoreductase on catalysis by CYP2D6 in vitro. | Sandee D | Pharmacogenetics and genomics | 2010 | PMID: 20940534 |
Ambiguous genitalia, impaired steroidogenesis, and Antley-Bixler syndrome in a patient with P450 oxidoreductase deficiency. | But WM | Hong Kong medical journal = Xianggang yi xue za zhi | 2010 | PMID: 20124576 |
Pharmacogenetics of P450 oxidoreductase: effect of sequence variants on activities of CYP1A2 and CYP2C19. | Agrawal V | Pharmacogenetics and genomics | 2008 | PMID: 18551037 |
POR R457H is a global founder mutation causing Antley-Bixler syndrome with autosomal recessive trait. | Adachi M | American journal of medical genetics. Part A | 2006 | PMID: 16470797 |
Diversity and function of mutations in p450 oxidoreductase in patients with Antley-Bixler syndrome and disordered steroidogenesis. | Huang N | American journal of human genetics | 2005 | PMID: 15793702 |
Cytochrome P450 oxidoreductase gene mutations and Antley-Bixler syndrome with abnormal genitalia and/or impaired steroidogenesis: molecular and clinical studies in 10 patients. | Fukami M | The Journal of clinical endocrinology and metabolism | 2005 | PMID: 15483095 |
Congenital adrenal hyperplasia caused by mutant P450 oxidoreductase and human androgen synthesis: analytical study. | Arlt W | Lancet (London, England) | 2004 | PMID: 15220035 |
Mutant P450 oxidoreductase causes disordered steroidogenesis with and without Antley-Bixler syndrome. | Flück CE | Nature genetics | 2004 | PMID: 14758361 |
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Text-mined citations for rs28931608 ...
HelpRecord last updated Nov 25, 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.