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NM_000440.3(PDE6A):c.878C>T (p.Pro293Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Oct 4, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000197670.10
Variation ID:
197670
Description:
single nucleotide variant
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NM_000440.3(PDE6A):c.878C>T (p.Pro293Leu)

Allele ID
194831
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q32
Genomic location
5: 149921690 (GRCh38) GRCh38 UCSC
5: 149301253 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P16499:p.Pro293Leu
NC_000005.10:g.149921690G>A
NC_000005.9:g.149301253G>A
... more HGVS
Protein change
P293L
Other names
-
Canonical SPDI
NC_000005.10:149921689:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00361
The Genome Aggregation Database (gnomAD) 0.00364
The Genome Aggregation Database (gnomAD) 0.00309
Trans-Omics for Precision Medicine (TOPMed) 0.00284
Trans-Omics for Precision Medicine (TOPMed) 0.00300
Exome Aggregation Consortium (ExAC) 0.00302
1000 Genomes Project 0.00180
The Genome Aggregation Database (gnomAD), exomes 0.00314
Links
ClinGen: CA203011
UniProtKB: P16499#VAR_025464
dbSNP: rs114973968
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Apr 10, 2015 RCV000178770.2
Likely benign 3 criteria provided, single submitter Dec 3, 2020 RCV000954915.5
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations May 28, 2019 RCV000787859.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PDE6A - - GRCh38
GRCh37
478 495

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230924.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa
Allele origin: unknown
Mendelics
Accession: SCV001137003.1
Submitted: (Oct 22, 2019)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001315121.1
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001101582.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001963496.1
Submitted: (Oct 04, 2021)
Evidence details
Likely pathogenic
(Apr 01, 2018)
no assertion criteria provided
Method: research
Retinitis pigmentosa
Allele origin: unknown
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet
Study: VeluxRD
Accession: SCV000926874.1
Submitted: (Dec 05, 2018)
Evidence details
Publications
PubMed (1)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001553642.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The PDE6A p.Pro293Leu variant was identified in the literature in two patients with retinitis pigementosa: in one case the variant was identfiied as a heterozygous … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
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: SCV001918169.1
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
Molecular genetic analysis using targeted NGS analysis of 677 individuals with retinal dystrophy. Jespersgaard C Scientific reports 2019 PMID: 30718709
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PDE6A - - - -

Text-mined citations for rs114973968...

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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 Nov 27, 2021