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NM_000539.3(RHO):c.886A>G (p.Lys296Glu) AND Retinitis pigmentosa 4

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jan 3, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000013905.25

Allele description [Variation Report for NM_000539.3(RHO):c.886A>G (p.Lys296Glu)]

NM_000539.3(RHO):c.886A>G (p.Lys296Glu)

Gene:
RHO:rhodopsin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_000539.3(RHO):c.886A>G (p.Lys296Glu)
HGVS:
  • NC_000003.12:g.129532722A>G
  • NG_009115.1:g.9084A>G
  • NM_000539.3:c.886A>GMANE SELECT
  • NP_000530.1:p.Lys296Glu
  • NC_000003.11:g.129251565A>G
  • P08100:p.Lys296Glu
Protein change:
K296E; LYS296GLU
Links:
UniProtKB: P08100#VAR_004828; OMIM: 180380.0016; dbSNP: rs29001653
NCBI 1000 Genomes Browser:
rs29001653
Molecular consequence:
  • NM_000539.3:c.886A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Retinitis pigmentosa 4 (RP4)
Synonyms:
RP 4; RETINITIS PIGMENTOSA, RHODOPSIN-RELATED
Identifiers:
MONDO: MONDO:0013395; MedGen: C3151001; Orphanet: 791; OMIM: 613731

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000034152OMIM
no assertion criteria provided
Pathogenic
(Oct 1, 1992)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV001443249Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 1, 2020)
germlineclinical testing

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

SCV0020586313billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 3, 2022)
germlineclinical testing

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

PMID:11139241

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Autosomal dominant retinitis pigmentosa: four new mutations in rhodopsin, one of them in the retinal attachment site.

Keen TJ, Inglehearn CF, Lester DH, Bashir R, Jay M, Bird AC, Jay B, Bhattacharya SS.

Genomics. 1991 Sep;11(1):199-205.

PubMed [citation]
PMID:
1765377

Constitutively active mutants of rhodopsin.

Robinson PR, Cohen GB, Zhukovsky EA, Oprian DD.

Neuron. 1992 Oct;9(4):719-25.

PubMed [citation]
PMID:
1356370
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000034152.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In a family with autosomal dominant retinitis pigmentosa (RP4; 613731), Keen et al. (1991) observed change in codon 296 from AAG to GAG resulting in substitution of glutamic acid for lysine. The disorder in this family was distinguished by its particular severity, showing early onset of the disease and development of cataracts by the third or fourth decade of life. Two critical amino acids in rhodopsin are lys296, the site of attachment of retinal to the protein through a protonated Schiff base linkage, and glu113, the Schiff base counterion. Robinson et al. (1992) demonstrated that mutation in lys296 or in glu113 results in constitutive activation of opsin, as assayed by its ability to activate the G protein transducin in the absence of added chromophore. They concluded that opsin is constrained to an inactive conformation by a salt bridge between lys296 and glu113. The lys296-to-glu (K296E) mutation in the family reported by Keen et al. (1991) may represent degeneration of the photoreceptor cells as a result of persistent stimulation of the phototransduction pathway.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals, SCV001443249.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

From 3billion, SCV002058631.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013030, PMID:1765377, PS1_S). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000955802,VCV000984768, PMID:11139241,NULL,31087526, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.835, 3CNET: 0.998, PP3_P). A missense variant is a common mechanism associated with Retinitis pigmentosa 4 (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Feb 20, 2024