ClinVar Genomic variation as it relates to human health
NM_000322.5(PRPH2):c.424C>T (p.Arg142Trp)
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_000322.5(PRPH2):c.424C>T (p.Arg142Trp)
Variation ID: 13183 Accession: VCV000013183.30
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6p21.1 6: 42721911 (GRCh38) [ NCBI UCSC ] 6: 42689649 (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 Feb 20, 2014 Mar 10, 2024 Dec 4, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000322.5:c.424C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000313.2:p.Arg142Trp missense NC_000006.12:g.42721911G>A NC_000006.11:g.42689649G>A NG_009176.2:g.5710C>T - Protein change
- R142W
- Other names
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- Canonical SPDI
- NC_000006.12:42721910: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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Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
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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PRPH2 | - | - |
GRCh38 GRCh37 |
748 | 760 |
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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Jun 1, 1996 | RCV000014071.39 | |
Pathogenic/Likely pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Mar 25, 2023 | RCV000084971.23 | |
Pathogenic (1) |
no assertion criteria provided
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Sep 1, 2016 | RCV000678606.13 | |
Pathogenic (2) |
criteria provided, single submitter
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Jan 7, 2020 | RCV001250318.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 7, 2020 | RCV001250320.9 | |
maculopathy
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Pathogenic (1) |
no assertion criteria provided
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Jun 23, 2019 | RCV001003149.9 |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Oct 1, 2023 | RCV001075677.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 7, 2020 | RCV001250319.9 | |
Pathogenic (1) |
no assertion criteria provided
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Apr 1, 2018 | RCV000787661.9 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 4, 2023 | RCV001061048.14 | |
Pathogenic/Likely pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Jul 15, 2022 | RCV001353001.12 | |
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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
(Jan 07, 2020)
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criteria provided, single submitter
Method: clinical testing
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Stargardt disease
Affected status: yes
Allele origin:
germline
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NEI Ophthalmic Genomics Laboratory, National Institutes of Health
Accession: SCV001424638.1
First in ClinVar: Jul 27, 2020 Last updated: Jul 27, 2020 |
Comment:
The variant NM_000322.4:c.424C>T in the PRPH2 gene has been previously studied(PMIDs 7875944, 22003107, 22334370, 28559085, 28076437, 29555955, 29155698, 30215852, 30910914). We found this variant in … (more)
The variant NM_000322.4:c.424C>T in the PRPH2 gene has been previously studied(PMIDs 7875944, 22003107, 22334370, 28559085, 28076437, 29555955, 29155698, 30215852, 30910914). We found this variant in 5 patient(s) in a PRPH2 cohort study (Reeves et al. 2020). This variant is listed in dbSNP and/or HGMD (rs61755783,CM951116). It is present in gnomAD browser (AF 0.0000163). It is enriched in the PRPH2 disease cohort. We invoked ACMG criteria [PS4, PM1, PM2, PP3, PP5] and classified NM_000322.4:c.424C>T in the PRPH2 gene as a Pathogenic mutation. (less)
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Pathogenic
(Jan 07, 2020)
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criteria provided, single submitter
Method: clinical testing
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Patterned dystrophy of the retinal pigment epithelium
Affected status: yes
Allele origin:
germline
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NEI Ophthalmic Genomics Laboratory, National Institutes of Health
Accession: SCV001424639.1
First in ClinVar: Jul 27, 2020 Last updated: Jul 27, 2020 |
Comment:
The variant NM_000322.4:c.424C>T in the PRPH2 gene has been previously studied(PMIDs 7875944, 22003107, 22334370, 28559085, 28076437, 29555955, 29155698, 30215852, 30910914). We found this variant in … (more)
The variant NM_000322.4:c.424C>T in the PRPH2 gene has been previously studied(PMIDs 7875944, 22003107, 22334370, 28559085, 28076437, 29555955, 29155698, 30215852, 30910914). We found this variant in 5 patient(s) in a PRPH2 cohort study (Reeves et al. 2020). This variant is listed in dbSNP and/or HGMD (rs61755783,CM951116). It is present in gnomAD browser (AF 0.0000163). It is enriched in the PRPH2 disease cohort. We invoked ACMG criteria [PS4, PM1, PM2, PP3, PP5] and classified NM_000322.4:c.424C>T in the PRPH2 gene as a Pathogenic mutation. (less)
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Pathogenic
(Jan 07, 2020)
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criteria provided, single submitter
Method: clinical testing
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Retinitis pigmentosa
Affected status: yes
Allele origin:
germline
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NEI Ophthalmic Genomics Laboratory, National Institutes of Health
Accession: SCV001424640.1
First in ClinVar: Jul 27, 2020 Last updated: Jul 27, 2020 |
Comment:
The variant NM_000322.4:c.424C>T in the PRPH2 gene has been previously studied(PMIDs 7875944, 22003107, 22334370, 28559085, 28076437, 29555955, 29155698, 30215852, 30910914). We found this variant in … (more)
The variant NM_000322.4:c.424C>T in the PRPH2 gene has been previously studied(PMIDs 7875944, 22003107, 22334370, 28559085, 28076437, 29555955, 29155698, 30215852, 30910914). We found this variant in 5 patient(s) in a PRPH2 cohort study (Reeves et al. 2020). This variant is listed in dbSNP and/or HGMD (rs61755783,CM951116). It is present in gnomAD browser (AF 0.0000163). It is enriched in the PRPH2 disease cohort. We invoked ACMG criteria [PS4, PM1, PM2, PP3, PP5] and classified NM_000322.4:c.424C>T in the PRPH2 gene as a Pathogenic mutation. (less)
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Likely pathogenic
(Mar 25, 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: SCV001782129.2
First in ClinVar: Aug 14, 2021 Last updated: Apr 01, 2023 |
Comment:
Considered a founder variant in individuals from the southeastern region of the Netherlands (Boon et al., 2009); Identified in individuals with autosomal dominant retinitis pigmentosa … (more)
Considered a founder variant in individuals from the southeastern region of the Netherlands (Boon et al., 2009); Identified in individuals with autosomal dominant retinitis pigmentosa (Neveling et al., 2012; Van Cauwenbergh et al., 2017); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 29555955, 34411390, 19243827, 34647987, 34828423, 23891399, 8644804, 22003107, 22334370, 28076437, 17653047, 11139263, 11801511, 19038374, 30910914, 31047497, 30215852, 29155698, 28559085, 30718709, 31456290, 32531846, 31589614, 33846575, 34906036, 33546218) (less)
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Pathogenic
(Dec 04, 2023)
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criteria provided, single submitter
Method: clinical testing
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PRPH2-related disorder
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001225772.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 142 of the PRPH2 protein … (more)
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 142 of the PRPH2 protein (p.Arg142Trp). This variant is present in population databases (rs61755783, gnomAD 0.006%). This missense change has been observed in individuals with autosomal dominant pattern dystrophy, mild central areolarchoroidal dystrophy, or other retinal disease (PMID: 8644804, 19038374, 19243827, 28076437, 28559085). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13183). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PRPH2 protein function. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 17, 2014)
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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: SCV000224193.5
First in ClinVar: Jun 28, 2015 Last updated: Jul 31, 2019 |
Number of individuals with the variant: 3
Sex: mixed
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Pathogenic
(Mar 27, 2019)
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criteria provided, single submitter
Method: clinical testing
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Retinal dystrophy
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV001241305.1
First in ClinVar: Apr 18, 2020 Last updated: Apr 18, 2020
Comment:
My Retina Tracker patient
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Likely pathogenic
(Jan 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Patterned macular dystrophy 1
Affected status: yes
Allele origin:
unknown
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Institute of Medical Molecular Genetics, University of Zurich
Accession: SCV001548094.1
First in ClinVar: Mar 28, 2021 Last updated: Mar 28, 2021 |
Method: long-range PCR
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Pathogenic
(Jul 15, 2022)
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criteria provided, single submitter
Method: clinical testing
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Patterned macular dystrophy 1
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002581028.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022
Comment:
ACMG criteria applied: PS4_VSTR, PM2_SUP, PP1, PP3
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Number of individuals with the variant: 1
Sex: male
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Pathogenic
(Oct 01, 2023)
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criteria provided, single submitter
Method: research
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Retinal dystrophy
Affected status: yes
Allele origin:
germline
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Dept Of Ophthalmology, Nagoya University
Accession: SCV004707355.1
First in ClinVar: Mar 10, 2024 Last updated: Mar 10, 2024 |
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Pathogenic
(Sep 01, 2016)
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no assertion criteria provided
Method: clinical testing
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Cone dystrophy
Affected status: yes
Allele origin:
unknown
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Accession: SCV000804691.2
First in ClinVar: Sep 10, 2018 Last updated: Sep 10, 2018 |
Number of individuals with the variant: 1
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Pathogenic
(Apr 01, 2018)
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no assertion criteria provided
Method: research
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Progressive cone dystrophy (without rod involvement)
Affected status: yes
Allele origin:
unknown
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Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet
Study: VeluxRD
Accession: SCV000926650.2 First in ClinVar: Jul 21, 2019 Last updated: Sep 03, 2023 |
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Pathogenic
(Jun 23, 2019)
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no assertion criteria provided
Method: research
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Maculopathy
Affected status: yes
Allele origin:
inherited
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Sharon lab, Hadassah-Hebrew University Medical Center
Accession: SCV001161218.1
First in ClinVar: Feb 16, 2020 Last updated: Feb 16, 2020 |
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Pathogenic
(May 14, 2021)
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no assertion criteria provided
Method: curation
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not provided
Affected status: yes
Allele origin:
germline
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Leiden Open Variation Database
Accession: SCV001745130.1
First in ClinVar: Jul 07, 2021 Last updated: Jul 07, 2021 |
Comment:
Curator: Global Variome, with Curator vacancy. Submitters to LOVD: Global Variome, with Curator vacancy, Johan den Dunnen, Kornelia Neveling, LOVD, Manon Peeters. Comment: Variant observed … (more)
Curator: Global Variome, with Curator vacancy. Submitters to LOVD: Global Variome, with Curator vacancy, Johan den Dunnen, Kornelia Neveling, LOVD, Manon Peeters. Comment: Variant observed de novo. (less)
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Pathogenic
(-)
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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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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001952688.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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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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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001973425.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
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Pathogenic
(Jun 01, 1996)
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no assertion criteria provided
Method: literature only
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CHOROIDAL DYSTROPHY, CENTRAL AREOLAR, 2
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000034318.5
First in ClinVar: Apr 04, 2013 Last updated: Jul 06, 2020 |
Comment on evidence:
In 11 affected members from 7 families with central areolar choroidal dystrophy (CACD2; 613105), Hoyng et al. (1996) identified heterozygosity for a 664C-T transition in … (more)
In 11 affected members from 7 families with central areolar choroidal dystrophy (CACD2; 613105), Hoyng et al. (1996) identified heterozygosity for a 664C-T transition in exon 1 of the PRPH2 gene, resulting in an arg142-to-trp (R142W) substitution. The mutation was also detected in a 65-year-old female family member who had 20/20 visual acuity bilaterally and no posterior pole abnormalities on ophthalmoscopy or fluorescein angiography. The mutation was not found in 7 other unaffected family members or in 200 control chromosomes. Boon et al. (2009) identified the R142W mutation in 98 patients with CACD from 45 different Dutch families and noted that 96 (98%) of the patients originated from the southeast region of the Netherlands. Analysis of CA repeat markers and SNPs near the PRPH2 gene in 3 large families carrying the R142W mutation revealed an approximately 519-kb shared chromosomal segment, strongly suggesting that R142W represents a founder mutation. Carrier frequency of R142W was analyzed in 57 asymptomatic controls over 70 years of age from the same region of the Netherlands; the mutation was found in a 76-year-old man who reported no visual disturbances, but who was found to have early stage II CACD on ophthalmoscopic examination and fundus autofluorescence imaging. (less)
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Pathogenic
(-)
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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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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001925732.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
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Pathogenic
(Apr 21, 2022)
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no assertion criteria provided
Method: research
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Patterned macular dystrophy 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana
Accession: SCV002500972.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
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Pathogenic
(Dec 13, 2022)
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no assertion criteria provided
Method: research
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Stargardt disease
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
biparental
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Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana
Accession: SCV002761253.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
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not provided
(-)
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no classification provided
Method: not provided
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not provided
Affected status: not provided
Allele origin:
unknown
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Retina International
Accession: SCV000117107.1
First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_RDS:c.424C>T
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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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PRPH2-Associated Macular Dystrophy in 4 Family Members with a Novel Mutation. | Choi H | Ophthalmic genetics | 2022 | PMID: 34906036 |
Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases. | Maggi J | International journal of molecular sciences | 2021 | PMID: 33546218 |
Genotype-phenotype associations in a large PRPH2-related retinopathy cohort. | Reeves MJ | Human mutation | 2020 | PMID: 32531846 |
A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC). | Sharon D | Human mutation | 2020 | PMID: 31456290 |
Molecular genetic analysis using targeted NGS analysis of 677 individuals with retinal dystrophy. | Jespersgaard C | Scientific reports | 2019 | PMID: 30718709 |
Genetic screening for macular dystrophies in patients clinically diagnosed with dry age-related macular degeneration. | Kersten E | Clinical genetics | 2018 | PMID: 30215852 |
Clinical and genetic characteristics of 251 consecutive patients with macular and cone/cone-rod dystrophy. | Birtel J | Scientific reports | 2018 | PMID: 29555955 |
BULL'S EYE MACULOPATHY WITH MUTATIONS IN RDS/PRPH2 AND ROM-1. | Essilfie JO | Retinal cases & brief reports | 2018 | PMID: 29155698 |
Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. | Stone EM | Ophthalmology | 2017 | PMID: 28559085 |
Diagnostic exome sequencing in 266 Dutch patients with visual impairment. | Haer-Wigman L | European journal of human genetics : EJHG | 2017 | PMID: 28224992 |
Mutations in Splicing Factor Genes Are a Major Cause of Autosomal Dominant Retinitis Pigmentosa in Belgian Families. | Van Cauwenbergh C | PloS one | 2017 | PMID: 28076437 |
Analysis of ELOVL4 and PRPH2 genes in Turkish Stargardt disease patients. | Bardak H | Genetics and molecular research : GMR | 2016 | PMID: 27813578 |
The efficacy of microarray screening for autosomal recessive retinitis pigmentosa in routine clinical practice. | van Huet RA | Molecular vision | 2015 | PMID: 25999674 |
Prevalence of mutations in eyeGENE probands with a diagnosis of autosomal dominant retinitis pigmentosa. | Sullivan LS | Investigative ophthalmology & visual science | 2013 | PMID: 23950152 |
Next-generation genetic testing for retinitis pigmentosa. | Neveling K | Human mutation | 2012 | PMID: 22334370 |
Central areolar choroidal dystrophy (CACD) and age-related macular degeneration (AMD): differentiating characteristics in multimodal imaging. | Smailhodzic D | Investigative ophthalmology & visual science | 2011 | PMID: 22003107 |
Central areolar choroidal dystrophy. | Boon CJ | Ophthalmology | 2009 | PMID: 19243827 |
Phenotypic variability and long-term follow-up of patients with known and novel PRPH2/RDS gene mutations. | Renner AB | American journal of ophthalmology | 2009 | PMID: 19038374 |
High prevalence of mutations in peripherin/RDS in autosomal dominant macular dystrophies in a Spanish population. | Gamundi MJ | Molecular vision | 2007 | PMID: 17653047 |
Central areolar choroidal dystrophy associated with dominantly inherited drusen. | Klevering BJ | The British journal of ophthalmology | 2002 | PMID: 11801511 |
Two novel mutations (Y141H; C214Y) and previously published mutation (R142W) in the RDS-peripherin gene in autosomal dominant macular dystrophies in Spanish families. | Trujillo MJ | Human mutation | 2001 | PMID: 11139263 |
Autosomal dominant central areolar choroidal dystrophy caused by a mutation in codon 142 in the peripherin/RDS gene. | Hoyng CB | American journal of ophthalmology | 1996 | PMID: 8644804 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PRPH2 | - | - | - | - |
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Text-mined citations for rs61755783 ...
HelpRecord last updated Sep 29, 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.