NM_001029883.3(PCARE):c.3048_3049del (p.Tyr1016_Arg1017delinsTer) AND Retinitis pigmentosa 54

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 23, 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:: RCV003153170.1

Allele description [Variation Report for NM_001029883.3(PCARE):c.3048_3049del (p.Tyr1016_Arg1017delinsTer)]

NM_001029883.3(PCARE):c.3048_3049del (p.Tyr1016_Arg1017delinsTer)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p23.2

Genomic location:

Preferred name:

NM_001029883.3(PCARE):c.3048_3049del (p.Tyr1016_Arg1017delinsTer)

HGVS:

NC_000002.12:g.29071214_29071215del
NG_021427.1:g.8048_8049del
NM_001029883.3:c.3048_3049delMANE SELECT
NP_001025054.1:p.Tyr1016_Arg1017delinsTer
NC_000002.11:g.29294080_29294081del

Molecular consequence:

NM_001029883.3:c.3048_3049del - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003842023	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 23, 2023)	unknown	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

SCV003842023

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 23, 2023)

unknown

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	unknown	yes	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 3billion, SCV003842023.1

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

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Mar 26, 2023

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