NM_000297.4(PKD2):c.1081C>T (p.Arg361Ter) AND Autosomal dominant polycystic kidney disease

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 12, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001869209.7

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:: Autosomal dominant polycystic kidney disease (ADPKD)
Identifiers:: MONDO: MONDO:0004691; MedGen: C0085413

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002133882	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 12, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17582161, 22863349, 23376035, 31740684, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002133882

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 12, 2023)

germline

clinical testing

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

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

Citations

PubMed

Comprehensive molecular diagnostics in autosomal dominant polycystic kidney disease.

Rossetti S, Consugar MB, Chapman AB, Torres VE, Guay-Woodford LM, Grantham JJ, Bennett WM, Meyers CM, Walker DL, Bae K, Zhang QJ, Thompson PA, Miller JP, Harris PC; CRISP Consortium..

J Am Soc Nephrol. 2007 Jul;18(7):2143-60. Epub 2007 Jun 20.

PubMed [citation]

PMID:: 17582161

Clinical utility of PKD2 mutation testing in a polycystic kidney disease cohort attending a specialist nephrology out-patient clinic.

Robinson C, Hiemstra TF, Spencer D, Waller S, Daboo L, Karet Frankl FE, Sandford RN.

BMC Nephrol. 2012 Aug 3;13:79. doi: 10.1186/1471-2369-13-79.

PubMed [citation]

PMID:: 22863349
PMCID:: PMC3502417

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV002133882.3

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

Description

This sequence change creates a premature translational stop signal (p.Arg361*) in the PKD2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PKD2 are known to be pathogenic (PMID: 17582161, 22863349). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with autosomal dominant polycystic kidney disease type 2 (PMID: 23376035, 31740684). ClinVar contains an entry for this variant (Variation ID: 636770). For these reasons, this variant has been classified 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: Sep 16, 2024

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