NM_000283.4(PDE6B):c.2193+1G>A AND Retinitis pigmentosa 40

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 8, 2021
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:: RCV000153667.12

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]

Observations:

Condition(s)

Name:: Retinitis pigmentosa 40 (RP40)
Identifiers:: MONDO: MONDO:0013429; MedGen: C3151107; Orphanet: 791; OMIM: 613801

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000804678	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	no assertion criteria provided	Pathogenic (Sep 1, 2016)	unknown	clinical testing
SCV001573522	Ocular Genomics Institute, Massachusetts Eye and Ear	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 8, 2021)	germline	research	PubMed (5) [See all records that cite these PMIDs] 28041643, 25097241, 7724547, 28224992, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000804678

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

no assertion criteria provided

Pathogenic
(Sep 1, 2016)

unknown

clinical testing

SCV001573522

Ocular Genomics Institute, Massachusetts Eye and Ear

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 8, 2021)

germline

research

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.

Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, et al.

Am J Hum Genet. 2017 Jan 5;100(1):75-90. doi: 10.1016/j.ajhg.2016.12.003. Epub 2016 Dec 29.

PubMed [citation]

PMID:: 28041643
PMCID:: PMC5223092

Dependable and efficient clinical utility of target capture-based deep sequencing in molecular diagnosis of retinitis pigmentosa.

Wang J, Zhang VW, Feng Y, Tian X, Li FY, Truong C, Wang G, Chiang PW, Lewis RA, Wong LJ.

Invest Ophthalmol Vis Sci. 2014 Aug 5;55(10):6213-23. doi: 10.1167/iovs.14-14936.

PubMed [citation]

PMID:: 25097241

See all PubMed Citations (5)

Details of each submission

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+, SCV000804678.2

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

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

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573522.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (5)

Description

The PDE6B c.2193+1G>A variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PP1, PP3. Based on this evidence we have classified this variant as Pathogenic.

#	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

Last Updated: Jun 29, 2024

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