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NM_000322.5(PRPH2):c.647C>T (p.Pro216Leu) AND PRPH2-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 14, 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:
RCV001063368.5

Allele description [Variation Report for NM_000322.5(PRPH2):c.647C>T (p.Pro216Leu)]

NM_000322.5(PRPH2):c.647C>T (p.Pro216Leu)

Gene:
PRPH2:peripherin 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.1
Genomic location:
Preferred name:
NM_000322.5(PRPH2):c.647C>T (p.Pro216Leu)
HGVS:
  • NC_000006.12:g.42704546G>A
  • NG_009176.2:g.23075C>T
  • NM_000322.5:c.647C>TMANE SELECT
  • NP_000313.2:p.Pro216Leu
  • NC_000006.11:g.42672284G>A
  • NG_009176.1:g.23075C>T
  • NM_000322.4:c.647C>T
Protein change:
P216L; PRO216LEU
Links:
OMIM: 179605.0003; dbSNP: rs61755806
NCBI 1000 Genomes Browser:
rs61755806
Molecular consequence:
  • NM_000322.5:c.647C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
PRPH2-related disorder
Synonyms:
PRPH2-Related Disorders; PRPH2-related condition
Identifiers:
MedGen: CN239395

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001228209Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 14, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in the human retinal degeneration slow gene in autosomal dominant retinitis pigmentosa.

Kajiwara K, Hahn LB, Mukai S, Travis GH, Berson EL, Dryja TP.

Nature. 1991 Dec 12;354(6353):480-3.

PubMed [citation]
PMID:
1684223

Mutations in Splicing Factor Genes Are a Major Cause of Autosomal Dominant Retinitis Pigmentosa in Belgian Families.

Van Cauwenbergh C, Coppieters F, Roels D, De Jaegere S, Flipts H, De Zaeytijd J, Walraedt S, Claes C, Fransen E, Van Camp G, Depasse F, Casteels I, de Ravel T, Leroy BP, De Baere E.

PLoS One. 2017;12(1):e0170038. doi: 10.1371/journal.pone.0170038.

PubMed [citation]
PMID:
28076437
PMCID:
PMC5226823
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001228209.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 216 of the PRPH2 protein (p.Pro216Leu). This variant is present in population databases (rs61755806, gnomAD 0.0009%). This missense change has been observed in individual(s) with autosomal dominant retinitis pigmentosa (PMID: 1684223, 28076437). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13164). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PRPH2 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects PRPH2 function (PMID: 12925772). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jul 15, 2024