NM_000297.4(PKD2):c.1081C>T (p.Arg361Ter) AND PKD2-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 4, 2024
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:: RCV004753041.1

Allele description [Variation Report for NM_000297.4(PKD2):c.1081C>T (p.Arg361Ter)]

NM_000297.4(PKD2):c.1081C>T (p.Arg361Ter)

Gene:

PKD2:polycystin 2, transient receptor potential cation channel [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q22.1

Genomic location:

Preferred name:

NM_000297.4(PKD2):c.1081C>T (p.Arg361Ter)

HGVS:

NC_000004.12:g.88038488C>T
NG_008604.1:g.35821C>T
NM_000297.4:c.1081C>TMANE SELECT
NP_000288.1:p.Arg361Ter
NC_000004.11:g.88959640C>T
NM_000297.3:c.1081C>T
NR_156488.2:n.1180C>T

Protein change:

R361*

Links:

dbSNP: rs1578130676

NCBI 1000 Genomes Browser:

rs1578130676

Molecular consequence:

NR_156488.2:n.1180C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000297.4:c.1081C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: PKD2-related disorder
Synonyms:: PKD2-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005362888	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Pathogenic (Sep 4, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005362888

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Pathogenic
(Sep 4, 2024)

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005362888.1

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

Description

The PKD2 c.1081C>T variant is predicted to result in premature protein termination (p.Arg361*). This variant has been reported in many individuals with polycystic kidney disease (Chung et al. 2006. PubMed ID: 17100995; Paavola et al. 2013. PubMed ID: 23376035; Kim et al. 2019. PubMed ID: 31740684; Moriyama et al. 2020. PubMed ID: 33141305; Durkie et al. 2020. PubMed ID: 33168999). This variant has not been reported in a large population database, indicating this variant is rare. This variant has been reported in ClinVar by many outside laboratories as pathogenic (ncbi.nlm.nih.gov/clinvar/variation/636770). Nonsense variants in PKD2 are expected to be pathogenic. This variant is interpreted as pathogenic.

#	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

Last Updated: Nov 30, 2024

ClinVar

Relating variation to medicine