NM_001029883.3(PCARE):c.1984dup (p.Thr662fs) AND Retinitis pigmentosa 54

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 25, 2022
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:: RCV002267629.1

Allele description [Variation Report for NM_001029883.3(PCARE):c.1984dup (p.Thr662fs)]

NM_001029883.3(PCARE):c.1984dup (p.Thr662fs)

Gene:

PCARE:photoreceptor cilium actin regulator [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

2p23.2

Genomic location:

Preferred name:

NM_001029883.3(PCARE):c.1984dup (p.Thr662fs)

HGVS:

NC_000002.12:g.29072278dup
NG_021427.1:g.6984dup
NM_001029883.3:c.1984dupMANE SELECT
NP_001025054.1:p.Thr662fs
NC_000002.11:g.29295144dup
NM_001029883.2:c.1984dup
NM_001029883.3:c.1984dupAMANE SELECT

Protein change:

T662fs

Links:

dbSNP: rs1667504255

NCBI 1000 Genomes Browser:

rs1667504255

Molecular consequence:

NM_001029883.3:c.1984dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Retinitis pigmentosa 54 (RP54)
Identifiers:: MONDO: MONDO:0013263; MedGen: C3150691; Orphanet: 791; OMIM: 613428

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002549765	Sydney Genome Diagnostics, Children's Hospital Westmead See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 25, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002549765

Sydney Genome Diagnostics, Children's Hospital Westmead

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 25, 2022)

germline

clinical testing

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

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Sydney Genome Diagnostics, Children's Hospital Westmead, SCV002549765.1

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

Description

This individual is homozygous for the c.1984dup variant in the PCARE gene. This frameshifting variant is predicted to create a premature stop codon p.(Thr662Asnfs*18) and may result in a null allele due to nonsense-mediated mRNA decay. The variant has not been reported in any population databases (i.e. gnomAD v2.1.1, ESP or dbSNP). This variant has been previously reported as pathogenic once in the ClinVar database (Variation ID: 856173). Other truncating variants downstream of this amino acid have been also described in the ClinVar database (accessed: 25/5/2022), indicating that loss of function is a well-established mechanism of disease for this gene. This variant is considered to be likely pathogenic according to the ACMG guidelines (evidence used: PVS1, PM2).

#	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: Jun 23, 2024

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