NM_001029883.3(PCARE):c.3604C>T (p.Arg1202Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 23, 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:: RCV001041302.9

Allele description [Variation Report for NM_001029883.3(PCARE):c.3604C>T (p.Arg1202Ter)]

NM_001029883.3(PCARE):c.3604C>T (p.Arg1202Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.2

Genomic location:

Preferred name:

NM_001029883.3(PCARE):c.3604C>T (p.Arg1202Ter)

HGVS:

NC_000002.12:g.29070658G>A
NG_021427.1:g.8604C>T
NM_001029883.3:c.3604C>TMANE SELECT
NP_001025054.1:p.Arg1202Ter
NC_000002.11:g.29293524G>A
NM_001029883.2:c.3604C>T

Protein change:

R1202*

Links:

dbSNP: rs748396645

NCBI 1000 Genomes Browser:

rs748396645

Molecular consequence:

NM_001029883.3:c.3604C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Rattus norvegicus deubiquitinating enzyme Ubp109 (ubp109) mRNA, complete cds
Rattus norvegicus deubiquitinating enzyme Ubp109 (ubp109) mRNA, complete cds
gi|6492121|gb|AF106657.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001204907	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 23, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 28763557, 20398886, 24339724, 26496393, 28492532
SCV001765342	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 14, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001204907

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 23, 2022)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV001765342

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 14, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

C2orf71 Mutations as a Frequent Cause of Autosomal-Recessive Retinitis Pigmentosa: Clinical Analysis and Presentation of 8 Novel Mutations.

Gerth-Kahlert C, Tiwari A, Hanson JVM, Batmanabane V, Traboulsi E, Pennesi ME, Al-Qahtani AA, Lam BL, Heckenlively J, Zweifel SA, Vincent A, Fierz F, Barthelmes D, Branham K, Khan N, Bahr A, Baehr L, Magyar I, Koller S, Azzarello-Burri S, Niedrist D, Heon E, et al.

Invest Ophthalmol Vis Sci. 2017 Aug 1;58(10):3840-3850. doi: 10.1167/iovs.17-21597.

PubMed [citation]

PMID:: 28763557

Discovery and functional analysis of a retinitis pigmentosa gene, C2ORF71.

Nishimura DY, Baye LM, Perveen R, Searby CC, Avila-Fernandez A, Pereiro I, Ayuso C, Valverde D, Bishop PN, Manson FD, Urquhart J, Stone EM, Slusarski DC, Black GC, Sheffield VC.

Am J Hum Genet. 2010 May 14;86(5):686-95. doi: 10.1016/j.ajhg.2010.03.005. Epub 2010 Apr 15.

PubMed [citation]

PMID:: 20398886
PMCID:: PMC2868997

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001204907.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 839525). This premature translational stop signal has been observed in individual(s) with PCARE-related retinal dystrophy (PMID: 28763557). This variant is present in population databases (rs748396645, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Arg1202*) in the PCARE gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCARE are known to be pathogenic (PMID: 20398886, 24339724, 26496393).

#	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

From GeneDx, SCV001765342.1

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Identified in an individual with retinitis pigmentosa who had an additional C2orf71 variant in published literature; segregation data was not included (Gerth-Kahlert et al., 2017); This variant is associated with the following publications: (PMID: 28763557)

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

Last Updated: Jun 23, 2024

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