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NM_001009944.3(PKD1):c.12061C>T (p.Arg4021Ter) AND Polycystic kidney disease

Germline classification:
Pathogenic (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001292276.3

Allele description [Variation Report for NM_001009944.3(PKD1):c.12061C>T (p.Arg4021Ter)]

NM_001009944.3(PKD1):c.12061C>T (p.Arg4021Ter)

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.12061C>T (p.Arg4021Ter)
HGVS:
  • NC_000016.10:g.2090751G>A
  • NG_005895.1:g.46446G>A
  • NG_008617.1:g.52470C>T
  • NM_000296.4:c.12058C>T
  • NM_001009944.3:c.12061C>TMANE SELECT
  • NP_000287.4:p.Arg4020Ter
  • NP_001009944.3:p.Arg4021Ter
  • LRG_487:g.46446G>A
  • NC_000016.9:g.2140752G>A
  • NM_001009944.2:c.12061C>T
Protein change:
R4020*
Links:
dbSNP: rs764431330
NCBI 1000 Genomes Browser:
rs764431330
Molecular consequence:
  • NM_000296.4:c.12058C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001009944.3:c.12061C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Polycystic kidney disease
Synonyms:
Polycystic kidney dysplasia; Kidney, Polycystic
Identifiers:
MONDO: MONDO:0020642; MeSH: D007690; MedGen: C0022680; OMIM: PS173900; Human Phenotype Ontology: HP:0000113

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001480961Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Pathogenicunknownclinical testing

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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), SCV001480961.1

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

Description

The PKD1 p.Arg4021* variant was identified in 7 of 2636 proband chromosomes (frequency: 0.003) from individuals or families with ADPKD and was not identified in 200 control chromosomes from healthy individuals (Audrezet 2012, Rossetti 2001, Rossetti 2007, Yu 2011, Hwang 2016). The variant was also identified in LOVD 3.0 (1x) and ADPKD Mutation Database (as definitely pathogenic). The variant was not identified in dbSNP, ClinVar, PKD1-LOVD, or the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The p.Arg4021* variant leads to a premature stop codon at position 4021, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the PKD1 gene are an established mechanism of disease in ADPKD and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.

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

Last Updated: Sep 16, 2024