NM_000322.5(PRPH2):c.638G>A (p.Cys213Tyr) AND PRPH2-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 24, 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:: RCV001052017.6

Allele description [Variation Report for NM_000322.5(PRPH2):c.638G>A (p.Cys213Tyr)]

NM_000322.5(PRPH2):c.638G>A (p.Cys213Tyr)

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.638G>A (p.Cys213Tyr)

HGVS:

NC_000006.12:g.42704555C>T
NG_009176.2:g.23066G>A
NM_000322.5:c.638G>AMANE SELECT
NP_000313.2:p.Cys213Tyr
NC_000006.11:g.42672293C>T
NG_009176.1:g.23066G>A
NM_000322.4:c.638G>A

Protein change:

C213Y

Links:

dbSNP: rs61755803

NCBI 1000 Genomes Browser:

rs61755803

Molecular consequence:

NM_000322.5:c.638G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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holo-[acyl-carrier-protein] synthase [Saccharomyces cerevisiae S288C]
holo-[acyl-carrier-protein] synthase [Saccharomyces cerevisiae S288C]
gi|6321284|ref|NP_011361.1|

Protein
acetyl-CoA carboxylase ACC1 [Saccharomyces cerevisiae S288C]
acetyl-CoA carboxylase ACC1 [Saccharomyces cerevisiae S288C]
gi|6324343|ref|NP_014413.1|

Protein
PREDICTED: Mus musculus piggyBac transposable element derived 5 (Pgbd5), transcr...
PREDICTED: Mus musculus piggyBac transposable element derived 5 (Pgbd5), transcript variant X1, mRNA
gi|1907187972|ref|XM_030243379.2|

Nucleotide
Perkinsus chesapeaki isolate A7-3cl large subunit ribosomal RNA gene, partial se...
Perkinsus chesapeaki isolate A7-3cl large subunit ribosomal RNA gene, partial sequence
gi|1205241903|gb|MF186928.1|

Nucleotide
Pseudomonas sp. strain 7.8.24E 16S ribosomal RNA gene, partial sequence
Pseudomonas sp. strain 7.8.24E 16S ribosomal RNA gene, partial sequence
gi|1314786036|gb|MG681257.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001216205	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 24, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11934323, 28559085, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001216205

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 24, 2023)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Butterfly-shaped pattern dystrophy: a genetic, clinical, and histopathological report.

Zhang K, Garibaldi DC, Li Y, Green WR, Zack DJ.

Arch Ophthalmol. 2002 Apr;120(4):485-90.

PubMed [citation]

PMID:: 11934323

Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease.

Stone EM, Andorf JL, Whitmore SS, DeLuca AP, Giacalone JC, Streb LM, Braun TA, Mullins RF, Scheetz TE, Sheffield VC, Tucker BA.

Ophthalmology. 2017 Sep;124(9):1314-1331. doi: 10.1016/j.ophtha.2017.04.008. Epub 2017 May 27.

PubMed [citation]

PMID:: 28559085
PMCID:: PMC5565704

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001216205.5

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

Description

For these reasons, this variant has been classified as Pathogenic. 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. ClinVar contains an entry for this variant (Variation ID: 98692). This missense change has been observed in individual(s) with autosomal dominant pattern dystrophy (PMID: 11934323, 28559085). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 213 of the PRPH2 protein (p.Cys213Tyr).

#	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: Sep 29, 2024

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