NM_000283.4(PDE6B):c.1699C>T (p.Gln567Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 22, 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:: RCV001234473.8

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001407123	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 22, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 24265693, 26766544, 30646425, 8394174, 8595886, 22334370, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001407123

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 22, 2023)

germline

clinical testing

PubMed (7)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

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

Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing.

Weisschuh N, Mayer AK, Strom TM, Kohl S, Glöckle N, Schubach M, Andreasson S, Bernd A, Birch DG, Hamel CP, Heckenlively JR, Jacobson SG, Kamme C, Kellner U, Kunstmann E, Maffei P, Reiff CM, Rohrschneider K, Rosenberg T, Rudolph G, Vámos R, Varsányi B, et al.

PLoS One. 2016;11(1):e0145951. doi: 10.1371/journal.pone.0145951.

PubMed [citation]

PMID:: 26766544
PMCID:: PMC4713063

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001407123.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

ClinVar contains an entry for this variant (Variation ID: 632445). For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with retinitis pigmentosa (PMID: 24265693, 26766544, 30646425). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Gln567*) in the PDE6B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PDE6B are known to be pathogenic (PMID: 8394174, 8595886, 22334370).

#	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: Oct 13, 2024

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