NM_000283.4(PDE6B):c.2193+1G>A AND PDE6B-related disorder

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 21, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003387510.3

Allele description [Variation Report for NM_000283.4(PDE6B):c.2193+1G>A]

NM_000283.4(PDE6B):c.2193+1G>A

Gene:

PDE6B:phosphodiesterase 6B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_000283.4(PDE6B):c.2193+1G>A

HGVS:

NC_000004.12:g.664945G>A
NG_009839.1:g.44372G>A
NG_009839.2:g.44374G>A
NM_000283.4:c.2193+1G>AMANE SELECT
NM_001145291.2:c.2193+1G>A
NM_001145292.2:c.1356+1G>A
NM_001350154.3:c.1356+1G>A
NM_001350155.3:c.1038+1G>A
NM_001379246.1:c.1356+1G>A
NM_001379247.1:c.1356+1G>A
NC_000004.11:g.658734G>A
NM_000283.3:c.2193+1G>A

Links:

dbSNP: rs727504075

NCBI 1000 Genomes Browser:

rs727504075

Molecular consequence:

NM_000283.4:c.2193+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001145291.2:c.2193+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001145292.2:c.1356+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001350154.3:c.1356+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001350155.3:c.1038+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001379246.1:c.1356+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001379247.1:c.1356+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: PDE6B-related disorder
Synonyms:: PDE6B-Related Disorders; PDE6B-related disease; PDE6B-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004099052	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 21, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004719596	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Pathogenic (Aug 5, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004099052

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 21, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004719596

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Pathogenic
(Aug 5, 2024)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004099052.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

PM3_Strong, PP1, PP3_Strong, PM2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV004719596.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The PDE6B c.2193+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been documented causative for autosomal recessive retinitis pigmentosa (arRP) (McLaughlin et al. 1995 PubMed ID: 7724547; Wang et al. 2014. PubMed ID: 25097241). This variant is reported in 0.015% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Variants that disrupt the consensus splice donor site in PDE6B are expected to be pathogenic. This variant is interpreted as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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