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NM_001029883.3(PCARE):c.2600C>T (p.Pro867Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000166760.14
Variation ID:
166760
Description:
single nucleotide variant
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NM_001029883.3(PCARE):c.2600C>T (p.Pro867Leu)

Allele ID
177344
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p23.2
Genomic location
2: 29071662 (GRCh38) GRCh38 UCSC
2: 29294528 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.29294528G>A
NC_000002.12:g.29071662G>A
NG_021427.1:g.7600C>T
... more HGVS
Protein change
P867L
Other names
-
Canonical SPDI
NC_000002.12:29071661:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00140
Exome Aggregation Consortium (ExAC) 0.00153
1000 Genomes Project 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00186
The Genome Aggregation Database (gnomAD), exomes 0.00194
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00184
Links
UniProtKB: A6NGG8#VAR_063396
ClinGen: CA233555
dbSNP: rs182248363
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 4, 2016 RCV000152890.3
Likely benign 1 criteria provided, single submitter Nov 19, 2015 RCV000625234.2
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001136691.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 5, 2020 RCV000879053.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCARE - - GRCh38
GRCh37
577 602

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 19, 2015)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa 54
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000744247.1
Submitted: (Apr 09, 2018)
Evidence details
Likely benign
(Nov 04, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000202314.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001296550.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (3)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001022062.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Feb 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001152214.7
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001919256.1
Submitted: (Sep 23, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Novel C2orf71 mutations account for ∼1% of cases in a large French arRP cohort. Audo I Human mutation 2011 PMID: 21412943
A survey of DNA variation of C2ORF71 in probands with progressive autosomal recessive retinal degeneration and controls. Sergouniotis PI Investigative ophthalmology & visual science 2011 PMID: 20811058
Mutations in C2ORF71 cause autosomal-recessive retinitis pigmentosa. Collin RW American journal of human genetics 2010 PMID: 20398884
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=C2orf71 - - - -
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PCARE - - - -

Text-mined citations for rs182248363...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021