NM_000297.4(PKD2):c.2420G>A (p.Arg807Gln) AND Polycystic kidney disease 2

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 17, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001001908.13

Allele description [Variation Report for NM_000297.4(PKD2):c.2420G>A (p.Arg807Gln)]

NM_000297.4(PKD2):c.2420G>A (p.Arg807Gln)

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.2420G>A (p.Arg807Gln)

HGVS:

NC_000004.12:g.88067959G>A
NG_008604.1:g.65292G>A
NM_000297.4:c.2420G>AMANE SELECT
NP_000288.1:p.Arg807Gln
NC_000004.11:g.88989111G>A
NM_000297.2:c.2420G>A
NM_000297.3:c.2420G>A
NR_156488.2:n.2398G>A
Q13563:p.Arg807Gln

Protein change:

R807Q

Links:

UniProtKB: Q13563#VAR_058830; dbSNP: rs147654263

NCBI 1000 Genomes Browser:

rs147654263

Molecular consequence:

NM_000297.4:c.2420G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_156488.2:n.2398G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Polycystic kidney disease 2 (PKD2)
Synonyms:: POLYCYSTIC KIDNEY DISEASE, ADULT, TYPE II; POLYCYSTIC KIDNEY DISEASE 2 WITH OR WITHOUT POLYCYSTIC LIVER DISEASE
Identifiers:: MONDO: MONDO:0013131; MedGen: C2751306; OMIM: 613095

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000451564	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12707387, 23300259, 22863349 Citation Link,
SCV001159661	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Dec 30, 2018)	germline	clinical testing	Citation Link,
SCV002812628	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 17, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000451564

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV001159661

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Benign
(Dec 30, 2018)

germline

clinical testing

Citation Link,

SCV002812628

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 17, 2022)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Genotype-renal function correlation in type 2 autosomal dominant polycystic kidney disease.

Magistroni R, He N, Wang K, Andrew R, Johnson A, Gabow P, Dicks E, Parfrey P, Torra R, San-Millan JL, Coto E, Van Dijk M, Breuning M, Peters D, Bogdanova N, Ligabue G, Albertazzi A, Hateboer N, Demetriou K, Pierides A, Deltas C, St George-Hyslop P, et al.

J Am Soc Nephrol. 2003 May;14(5):1164-74.

PubMed [citation]

PMID:: 12707387

Epidemiology of autosomal-dominant polycystic kidney disease: an in-depth clinical study for south-western Germany.

Neumann HP, Jilg C, Bacher J, Nabulsi Z, Malinoc A, Hummel B, Hoffmann MM, Ortiz-Bruechle N, Glasker S, Pisarski P, Neeff H, Krämer-Guth A, Cybulla M, Hornberger M, Wilpert J, Funk L, Baumert J, Paatz D, Baumann D, Lahl M, Felten H, Hausberg M, et al.

Nephrol Dial Transplant. 2013 Jun;28(6):1472-87. doi: 10.1093/ndt/gfs551. Epub 2013 Jan 8.

PubMed [citation]

PMID:: 23300259

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000451564.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001159661.1

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

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002812628.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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