ClinVar Genomic variation as it relates to human health
NM_000322.5(PRPH2):c.929G>A (p.Arg310Lys)
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
-
NM_000322.5(PRPH2):c.929G>A (p.Arg310Lys)
Variation ID: 138905 Accession: VCV000138905.28
- Type and length
-
single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6p21.1 6: 42698407 (GRCh38) [ NCBI UCSC ] 6: 42666145 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Oct 2, 2016 Mar 10, 2024 Jan 31, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000322.5:c.929G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000313.2:p.Arg310Lys missense NC_000006.12:g.42698407C>T NC_000006.11:g.42666145C>T NG_009176.2:g.29214G>A - Protein change
- R310K
- Other names
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p.R310K:AGG>AAG
- Canonical SPDI
- NC_000006.12:42698406: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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0.05871 (C)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.93281
1000 Genomes Project 0.94129
1000 Genomes Project 30x 0.94129
Exome Aggregation Consortium (ExAC) 0.91168
The Genome Aggregation Database (gnomAD), exomes 0.91234
The Genome Aggregation Database (gnomAD) 0.92861
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.93072
- 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
Help
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 |
752 | 764 |
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. |
---|---|---|---|---|
Benign (7) |
criteria provided, multiple submitters, no conflicts
|
Apr 28, 2014 | RCV000153780.25 | |
Benign (1) |
criteria provided, single submitter
|
Jan 12, 2018 | RCV000277056.13 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
|
Oct 25, 2021 | RCV000328116.15 | |
Benign (1) |
criteria provided, single submitter
|
Jan 12, 2018 | RCV000382760.13 | |
Benign (3) |
criteria provided, multiple submitters, no conflicts
|
Oct 25, 2021 | RCV000273176.16 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
|
Oct 25, 2021 | RCV000332083.15 | |
Benign (1) |
criteria provided, single submitter
|
Jan 12, 2018 | RCV000367746.13 | |
Benign (1) |
criteria provided, single submitter
|
Jan 31, 2024 | RCV001511184.15 | |
Benign (1) |
criteria provided, single submitter
|
Oct 25, 2021 | RCV001789197.10 | |
Benign (1) |
criteria provided, single submitter
|
Oct 25, 2021 | RCV001789198.10 | |
Benign (1) |
criteria provided, single submitter
|
Nov 22, 2023 | RCV003114279.11 | |
Benign (1) |
criteria provided, single submitter
|
Oct 1, 2023 | RCV003888535.1 | |
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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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Benign
(-)
|
criteria provided, single submitter
Method: clinical testing
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NOT SPECIFIED
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV000303597.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
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Benign
(Apr 28, 2014)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000203356.7
First in ClinVar: Jan 29, 2015 Last updated: Oct 02, 2016 |
Number of individuals with the variant: 3
Zygosity: Homozygote, Single Heterozygote
Sex: mixed
|
|
Benign
(Oct 01, 2023)
|
criteria provided, single submitter
Method: research
|
Retinal dystrophy
Affected status: yes
Allele origin:
germline
|
Dept Of Ophthalmology, Nagoya University
Accession: SCV004707321.1
First in ClinVar: Mar 10, 2024 Last updated: Mar 10, 2024 |
|
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Benign
(Jun 28, 2011)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000171334.10
First in ClinVar: Jun 23, 2014 Last updated: Oct 02, 2016 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
|
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Benign
(May 28, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Patterned macular dystrophy 1
Affected status: unknown
Allele origin:
unknown
|
Mendelics
Accession: SCV001137111.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
|
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Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
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Cone-rod dystrophy
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000463251.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Pigmentary retinal dystrophy
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000463247.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Patterned macular dystrophy 1
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000463249.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Choroidal dystrophy, central areolar 2
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000463250.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Vitelliform macular dystrophy 3
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000463248.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Retinitis pigmentosa
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000463246.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Benign
(Oct 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Choroidal dystrophy, central areolar 2
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002031934.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021 |
|
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Benign
(Oct 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Retinitis pigmentosa 7
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002031935.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021 |
|
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Benign
(Oct 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Patterned macular dystrophy 1
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002031936.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021 |
|
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Benign
(Oct 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Vitelliform macular dystrophy 3
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002031937.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021 |
|
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Benign
(Oct 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Pigmentary retinal dystrophy
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002031938.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021 |
|
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Benign
(Nov 22, 2023)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV003799807.3
First in ClinVar: Feb 13, 2023 Last updated: Feb 20, 2024 |
|
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Benign
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
|
PRPH2-related disorder
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001718383.4
First in ClinVar: Jun 15, 2021 Last updated: Feb 28, 2024 |
|
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Likely benign
(Mar 21, 2021)
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no assertion criteria provided
Method: curation
|
not specified
Affected status: yes
Allele origin:
germline
|
Leiden Open Variation Database
Accession: SCV001745129.1
First in ClinVar: Jul 07, 2021 Last updated: Jul 07, 2021 |
Comment:
Curator: Global Variome, with Curator vacancy. Submitters to LOVD: Julia Lopez, Yoshito Koyanagi.
|
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Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742561.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
|
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Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
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: SCV001963740.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
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Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
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: SCV001957999.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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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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Genetic characteristics of retinitis pigmentosa in 1204 Japanese patients. | Koyanagi Y | Journal of medical genetics | 2019 | PMID: 31213501 |
Peripherin/RDS and VMD2 mutations in macular dystrophies with adult-onset vitelliform lesion. | Zhuk SA | Molecular vision | 2006 | PMID: 16885924 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PRPH2 | - | - | - | - |
Text-mined citations for rs425876 ...
HelpRecord last updated Nov 30, 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.