NM_001029883.3(PCARE):c.1114G>A (p.Asp372Asn) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Nov 4, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001247310.2

Allele description [Variation Report for NM_001029883.3(PCARE):c.1114G>A (p.Asp372Asn)]

NM_001029883.3(PCARE):c.1114G>A (p.Asp372Asn)

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.1114G>A (p.Asp372Asn)
HGVS:
  • NC_000002.12:g.29073148C>T
  • NG_021427.1:g.6114G>A
  • NM_001029883.3:c.1114G>AMANE SELECT
  • NP_001025054.1:p.Asp372Asn
  • NC_000002.11:g.29296014C>T
  • NM_001029883.2:c.1114G>A
Protein change:
D372N
Links:
dbSNP: rs201284350
NCBI 1000 Genomes Browser:
rs201284350
Molecular consequence:
  • NM_001029883.3:c.1114G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001367888Centre for Mendelian Genomics,University Medical Centre Ljubljanacriteria provided, single submitter
Uncertain significance
(May 4, 2019)
unknownclinical testing

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

SCV001420722Invitaecriteria provided, single submitter
Uncertain significance
(Nov 4, 2019)
germlineclinical testing

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

Summary from all submissions

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Centre for Mendelian Genomics,University Medical Centre Ljubljana, SCV001367888.2

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

Description

This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PM2,PP5.

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

From Invitae, SCV001420722.1

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

Description

This sequence change replaces aspartic acid with asparagine at codon 372 of the PCARE protein (p.Asp372Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine. This variant is present in population databases (rs201284350, ExAC 0.009%). This variant has not been reported in the literature in individuals with PCARE-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Jan 16, 2021

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