NM_000283.4(PDE6B):c.1678C>T (p.Arg560Cys) AND Retinitis pigmentosa 40

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 1, 2015
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000201856.3

Allele description [Variation Report for NM_000283.4(PDE6B):c.1678C>T (p.Arg560Cys)]

NM_000283.4(PDE6B):c.1678C>T (p.Arg560Cys)

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.1678C>T (p.Arg560Cys)

HGVS:

NC_000004.12:g.662197C>T
NG_009839.1:g.41624C>T
NM_000283.4:c.1678C>TMANE SELECT
NM_001145291.2:c.1678C>T
NM_001145292.2:c.841C>T
NM_001350154.3:c.841C>T
NM_001350155.3:c.523C>T
NM_001379246.1:c.841C>T
NM_001379247.1:c.841C>T
NP_000274.2:p.Arg560Cys
NP_000274.3:p.Arg560Cys
NP_001138763.2:p.Arg560Cys
NP_001138764.2:p.Arg281Cys
NP_001337083.1:p.Arg281Cys
NP_001337084.1:p.Arg175Cys
NP_001366175.1:p.Arg281Cys
NP_001366176.1:p.Arg281Cys
NC_000004.11:g.655986C>T
NM_000283.3:c.1678C>T

Protein change:

R175C; ARG560CYS

Links:

OMIM: 180072.0008; dbSNP: rs201541131

NCBI 1000 Genomes Browser:

rs201541131

Molecular consequence:

NM_000283.4:c.1678C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001145291.2:c.1678C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001145292.2:c.841C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350154.3:c.841C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350155.3:c.523C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379246.1:c.841C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379247.1:c.841C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000256603	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 2015)	germline	literature only	PubMed (3) [See all records that cite these PMIDs] 12525556, 25823529, 17267005

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000256603

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 2015)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa: high prevalence and phenotypic variation.

Bernal S, Ayuso C, Antiñolo G, Gimenez A, Borrego S, Trujillo MJ, Marcos I, Calaf M, Del Rio E, Baiget M.

J Med Genet. 2003 Jan;40(1):e8. No abstract available.

PubMed [citation]

PMID:: 12525556
PMCID:: PMC1735247

Re-evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F.

Pozo MG, Bravo-Gil N, Méndez-Vidal C, Montero-de-Espinosa I, Millán JM, Dopazo J, Borrego S, Antiñolo G.

Am J Med Genet A. 2015 Jul;167(7):1597-600. doi: 10.1002/ajmg.a.37003. Epub 2015 Mar 30.

PubMed [citation]

PMID:: 25823529

See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000256603.3

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

Description

By next-generation sequencing in 1 of 2 Spanish sibs (family S23) with retinitis pigmentosa (RP40; 613801), previously reported by Bernal et al. (2003), Pozo et al. (2015) identified a homozygous c.1678C-T transition in exon 16 of the PDE6B gene, resulting in an arg560-to-cys (R560C) substitution at a conserved residue in a domain responsible for the catalytic function of the protein. The mutation segregated with the disease in the family and was absent in 200 control individuals. The authors noted that an R560C mutation was previously identified in the Pde6b-rd10 mutant mouse by Chang et al. (2007). In the S23 family, Bernal et al. (2003) had identified a homozygous mutation in the USH2A gene (C759F; 608400.0006) in the 2 affected sibs as well as in 2 of their unaffected sibs, indicating that the C759F mutation was not causative.

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

Last Updated: Sep 29, 2024

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