ClinVar Genomic variation as it relates to human health
NM_006269.2(RP1):c.2029C>T (p.Arg677Ter)
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_006269.2(RP1):c.2029C>T (p.Arg677Ter)
Variation ID: 5965 Accession: VCV000005965.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8q12.1 8: 54625911 (GRCh38) [ NCBI UCSC ] 8: 55538471 (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 Apr 20, 2016 Mar 10, 2024 Jan 29, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_006269.2:c.2029C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_006260.1:p.Arg677Ter nonsense NC_000008.11:g.54625911C>T NC_000008.10:g.55538471C>T NG_009840.2:g.14845C>T - Protein change
- R677*
- Other names
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- Canonical SPDI
- NC_000008.11:54625910: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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Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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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RP1 | - | - |
GRCh38 GRCh37 |
1270 | 1533 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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 (3) |
criteria provided, multiple submitters, no conflicts
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Feb 3, 2022 | RCV000006329.9 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Jan 29, 2024 | RCV000255140.17 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Oct 1, 2023 | RCV001074787.3 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
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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
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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
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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
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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
(Apr 08, 2021)
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criteria provided, single submitter
Method: research
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Retinitis pigmentosa 1
Affected status: yes
Allele origin:
germline
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Ocular Genomics Institute, Massachusetts Eye and Ear
Accession: SCV001573274.1
First in ClinVar: May 10, 2021 Last updated: May 10, 2021 |
Comment:
The RP1 c.2029C>T variant was identified in an individual with retinitis pigmentosa with a presumed dominant inheritance pattern. Through a review of available evidence we … (more)
The RP1 c.2029C>T variant was identified in an individual with retinitis pigmentosa with a presumed dominant inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PS3, PM2, PP1. Based on this evidence we have classified this variant as Pathogenic. (less)
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Pathogenic
(Feb 03, 2022)
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criteria provided, single submitter
Method: clinical testing
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Retinitis pigmentosa 1
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002761867.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
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Pathogenic
(Jan 29, 2024)
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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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Invitae
Accession: SCV001234444.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg677*) in the RP1 gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Arg677*) in the RP1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1480 amino acid(s) of the RP1 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with autosomal dominant retinitis pigmentosa (adRP) (PMID: 10391211, 29847639). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5965). This variant disrupts the C-terminus of the RP1 protein. Many variants that disrupt this region have been reported in individuals with either autosomal dominant or autosomal recessive retinitis pigmentosa (PMID: 11527933, 19933189, 29425069, 30027431, 33681214). Therefore, variants that disrupt this region are expected to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jul 25, 2013)
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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: SCV000113299.8
First in ClinVar: Jan 17, 2014 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 3
Sex: mixed
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Pathogenic
(Jul 07, 2018)
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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: SCV000322378.7
First in ClinVar: Oct 09, 2016 Last updated: Apr 17, 2019 |
Comment:
The R677X variant in the RP1 gene has been reported previously in association with autosomal dominant retinitis pigmentosa (Pierce et al., 1999; Guillonneau et al., … (more)
The R677X variant in the RP1 gene has been reported previously in association with autosomal dominant retinitis pigmentosa (Pierce et al., 1999; Guillonneau et al., 1999; Sullivan et al., 1999). This variant is predicted to cause loss of normal protein function through protein truncation. The R677X variant is not observed in large population cohorts (Lek et al., 2016). We interpret R677X as a pathogenic variant. (less)
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Pathogenic
(Jun 24, 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: SCV001240383.1
First in ClinVar: Apr 18, 2020 Last updated: Apr 18, 2020
Comment:
My Retina Tracker patient
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Pathogenic
(Oct 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
(Autosomal unknown)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001446675.1
First in ClinVar: Nov 28, 2020 Last updated: Nov 28, 2020 |
Clinical Features:
Rod-cone dystrophy (present)
Sex: female
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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: SCV004706079.1
First in ClinVar: Mar 10, 2024 Last updated: Mar 10, 2024 |
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Pathogenic
(Aug 01, 1999)
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no assertion criteria provided
Method: literature only
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RETINITIS PIGMENTOSA 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000026511.3
First in ClinVar: Apr 04, 2013 Last updated: Feb 20, 2021 |
Comment on evidence:
In a patient with retinitis pigmentosa (RP1; 180100), Pierce et al. (1999) found a C-to-T transition in exon 4 of the RP1 gene, resulting in … (more)
In a patient with retinitis pigmentosa (RP1; 180100), Pierce et al. (1999) found a C-to-T transition in exon 4 of the RP1 gene, resulting in a nonsense mutation, CGA (arg) to TGA (ter). This mutant allele, if expressed, would encode a protein of 676 amino acids, 1,480 less than the predicted wildtype RP1 protein. The mutation was first identified in the family in which Blanton et al. (1991) identified linkage to chromosome 8. The first member of the family studied was the offspring of 2 affected parents who were distantly related and presumed to carry the same RP1 mutation. The patient was found to be homozygous for the R677X mutation as was one of her sibs. Analysis of codon 677 in 17 other family members revealed that all of these affected members were heterozygotes. This family was also studied by Sullivan et al. (1999), who reported that the homozygotes were unusually severely affected. Pierce et al. (1999) evaluated 242 patients with autosomal dominant RP from separate families across the United States and Canada for the R677X mutation. Patients with known mutations in other dominant RP genes, RHO (180380) or RDS (PRPH2; 179605), were excluded from this analysis. They found 10 patients who were heterozygous for the R677X mutation. All 10 patients, who were examined at an age ranging from 35 to 49 years, with the mean age being 41.7 years, had findings typical of retinitis pigmentosa: night blindness as an early symptom, constricted visual fields, and funduscopic findings of attenuated vessels and intraretinal pigmentation. Pierce et al. (1999) reported that this mutation was present in approximately 3% of cases of autosomal dominant retinitis pigmentosa in North America. In affected members of an Australian RP1 family (family D), previously studied by Xu et al. (1996), Sullivan et al. (1999) identified heterozygosity for the same R677X mutation in the RP1 gene as had been found in the UCLA-RP01 family. Sullivan et al. (1999) noted that 2 distinct haplotypes segregated with disease in the 2 families, suggesting that the families were not related or that the mutation was very old. In a family with autosomal dominant retinitis pigmentosa reported by Iannaccone et al. (1996) to be linked to 8q, Guillonneau et al. (1999) identified the R677X mutation in the RP1 gene. (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: SCV001923614.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 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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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: SCV001956734.1 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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Dominant RP in the Middle While Recessive in Both the N- and C-Terminals Due to RP1 Truncations: Confirmation, Refinement, and Questions. | Wang J | Frontiers in cell and developmental biology | 2021 | PMID: 33681214 |
Clinical and genetic findings of a Japanese patient with RP1-related autosomal recessive retinitis pigmentosa. | Kurata K | Documenta ophthalmologica. Advances in ophthalmology | 2018 | PMID: 30027431 |
Toward the Mutational Landscape of Autosomal Dominant Retinitis Pigmentosa: A Comprehensive Analysis of 258 Spanish Families. | Martin-Merida I | Investigative ophthalmology & visual science | 2018 | PMID: 29847639 |
Targeted Next-Generation Sequencing Reveals Novel RP1 Mutations in Autosomal Recessive Retinitis Pigmentosa. | Li S | Genetic testing and molecular biomarkers | 2018 | PMID: 29425069 |
Compound heterozygosity of two novel truncation mutations in RP1 causing autosomal recessive retinitis pigmentosa. | Chen LJ | Investigative ophthalmology & visual science | 2010 | PMID: 19933189 |
Clinical features and mutations in patients with dominant retinitis pigmentosa-1 (RP1). | Berson EL | Investigative ophthalmology & visual science | 2001 | PMID: 11527933 |
A nonsense mutation in a novel gene is associated with retinitis pigmentosa in a family linked to the RP1 locus. | Guillonneau X | Human molecular genetics | 1999 | PMID: 10401003 |
Mutations in a novel retina-specific gene cause autosomal dominant retinitis pigmentosa. | Sullivan LS | Nature genetics | 1999 | PMID: 10391212 |
Mutations in a gene encoding a new oxygen-regulated photoreceptor protein cause dominant retinitis pigmentosa. | Pierce EA | Nature genetics | 1999 | PMID: 10391211 |
Genetic mapping of RP1 on 8q11-q21 in an Australian family with autosomal dominant retinitis pigmentosa reduces the critical region to 4 cM between D8S601 and D8S285. | Xu SY | Human genetics | 1996 | PMID: 8931712 |
Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8. | Blanton SH | Genomics | 1991 | PMID: 1783394 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=RP1 | - | - | - | - |
Iannaccone, A., Cideciyan, A. V., Sheffield, V. C., Stone, E. M., Jacobson, S. G. Phenotype of chromosome 8q-linked autosomal dominant retinitis pigmentosa. (Abstract) Invest. Ophthal. Vis. Sci. 37: S345-only, 1996. | - | - | - | - |
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Text-mined citations for rs104894082 ...
HelpRecord last updated Sep 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.