NM_000283.4(PDE6B):c.1699C>T (p.Gln567Ter) AND Retinitis pigmentosa

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 1, 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:: RCV001724153.3

Allele description [Variation Report for NM_000283.4(PDE6B):c.1699C>T (p.Gln567Ter)]

NM_000283.4(PDE6B):c.1699C>T (p.Gln567Ter)

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.1699C>T (p.Gln567Ter)

HGVS:

NC_000004.12:g.662218C>T
NG_009839.1:g.41645C>T
NM_000283.4:c.1699C>TMANE SELECT
NM_001145291.2:c.1699C>T
NM_001145292.2:c.862C>T
NM_001350154.3:c.862C>T
NM_001350155.3:c.544C>T
NM_001379246.1:c.862C>T
NM_001379247.1:c.862C>T
NP_000274.2:p.Gln567Ter
NP_000274.3:p.Gln567Ter
NP_001138763.2:p.Gln567Ter
NP_001138764.2:p.Gln288Ter
NP_001337083.1:p.Gln288Ter
NP_001337084.1:p.Gln182Ter
NP_001366175.1:p.Gln288Ter
NP_001366176.1:p.Gln288Ter
NC_000004.11:g.656007C>T
NM_000283.3:c.1699C>T

Protein change:

Q182*

Links:

dbSNP: rs772057239

NCBI 1000 Genomes Browser:

rs772057239

Molecular consequence:

NM_000283.4:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001145291.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001145292.2:c.862C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350154.3:c.862C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350155.3:c.544C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001379246.1:c.862C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001379247.1:c.862C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001950315	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 1, 2021)	germline	curation	PubMed (3) [See all records that cite these PMIDs] 24265693, 25741868, 34906470

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001950315

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 1, 2021)

germline

curation

PubMed (3)
[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	germline	yes	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies.

Eisenberger T, Neuhaus C, Khan AO, Decker C, Preising MN, Friedburg C, Bieg A, Gliem M, Charbel Issa P, Holz FG, Baig SM, Hellenbroich Y, Galvez A, Platzer K, Wollnik B, Laddach N, Ghaffari SR, Rafati M, Botzenhart E, Tinschert S, Börger D, Bohring A, et al.

PLoS One. 2013;8(11):e78496. doi: 10.1371/journal.pone.0078496. Erratum in: PLoS One. 2014;9(11):e108840.

PubMed [citation]

PMID:: 24265693
PMCID:: PMC3827063

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

See all PubMed Citations (3)

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001950315.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (3)

Description

The p.Gln567Ter variant in PDE6B was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3-P. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.

#	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: Nov 10, 2024

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