NM_000297.4(PKD2):c.1774C>T (p.Arg592Ter) AND Autosomal dominant polycystic kidney disease

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 4, 2017
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:: RCV000556150.7

Allele description [Variation Report for NM_000297.4(PKD2):c.1774C>T (p.Arg592Ter)]

NM_000297.4(PKD2):c.1774C>T (p.Arg592Ter)

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.1774C>T (p.Arg592Ter)

HGVS:

NC_000004.12:g.88056143C>T
NG_008604.1:g.53476C>T
NM_000297.4:c.1774C>TMANE SELECT
NP_000288.1:p.Arg592Ter
NC_000004.11:g.88977295C>T
NM_000297.3:c.1774C>T
NR_156488.2:n.1873C>T

Protein change:

R592*

Links:

dbSNP: rs1553926905

NCBI 1000 Genomes Browser:

rs1553926905

Molecular consequence:

NR_156488.2:n.1873C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000297.4:c.1774C>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
SCV000658968	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 4, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22508176, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000658968

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 4, 2017)

germline

clinical testing

PubMed (2)
[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

Autosomal dominant polycystic kidney disease: comprehensive mutation analysis of PKD1 and PKD2 in 700 unrelated patients.

Audrézet MP, Cornec-Le Gall E, Chen JM, Redon S, Quéré I, Creff J, Bénech C, Maestri S, Le Meur Y, Férec C.

Hum Mutat. 2012 Aug;33(8):1239-50. doi: 10.1002/humu.22103. Epub 2012 May 24.

PubMed [citation]

PMID:: 22508176

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000658968.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal at codon 592 (p.Arg592*) of 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. This particular variant has been reported in the literature in two individuals affected with polycystic kidney disease (PMID: 22508176). 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: May 12, 2024

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