NM_001009944.3(PKD1):c.2879G>A (p.Gly960Asp) AND Polycystic kidney disease

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001292068.1

Allele description [Variation Report for NM_001009944.3(PKD1):c.2879G>A (p.Gly960Asp)]

NM_001009944.3(PKD1):c.2879G>A (p.Gly960Asp)

Gene:
PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001009944.3(PKD1):c.2879G>A (p.Gly960Asp)
HGVS:
  • NC_000016.10:g.2113267C>T
  • NG_008617.1:g.27632G>A
  • NM_000296.4:c.2879G>A
  • NM_001009944.3:c.2879G>AMANE SELECT
  • NP_000287.4:p.Gly960Asp
  • NP_001009944.3:p.Gly960Asp
  • NC_000016.9:g.2163268C>T
  • NM_000296.3:c.2879G>A
  • NM_001009944.2:c.2879G>A
Protein change:
G960D
Links:
dbSNP: rs1567208088
NCBI 1000 Genomes Browser:
rs1567208088
Molecular consequence:
  • NM_000296.4:c.2879G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001009944.3:c.2879G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Polycystic kidney disease
Synonyms:
Polycystic kidney dysplasia; Enlarged polycystic kidneys; Polycystic kidneys
Identifiers:
MONDO: MONDO:0020642; MedGen: C0022680; OMIM: PS173900; Human Phenotype Ontology: HP:0000113

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001480783Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001480783.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PKD1 p.Gly960Asp variant was identified in 1 of 460 proband chromosomes (frequency: 0.002) from individuals or families with ADPKD (Rossetti 2012). The variant was also identified in ADPKD Mutation Database (as likely pathogenic) but was not identified in dbSNP, ClinVar, GeneInsight-COGR, or LOVD 3.0, PKD1-LOVD databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Gly960 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Oct 8, 2021

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