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NM_000297.4(PKD2):c.2208_2213del (p.Leu736_Asn737del) AND Polycystic kidney disease

Germline classification:
Likely 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:
RCV001292008.2

Allele description [Variation Report for NM_000297.4(PKD2):c.2208_2213del (p.Leu736_Asn737del)]

NM_000297.4(PKD2):c.2208_2213del (p.Leu736_Asn737del)

Gene:
PKD2:polycystin 2, transient receptor potential cation channel [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4q22.1
Genomic location:
Preferred name:
NM_000297.4(PKD2):c.2208_2213del (p.Leu736_Asn737del)
HGVS:
  • NC_000004.12:g.88065463_88065468del
  • NG_008604.1:g.62796_62801del
  • NM_000297.4:c.2208_2213delMANE SELECT
  • NP_000288.1:p.Leu736_Asn737del
  • NC_000004.11:g.88986613_88986618del
  • NC_000004.11:g.88986615_88986620del
  • NM_000297.3:c.2208_2213del
  • NM_000297.3:c.2208_2213delAAACTT
  • NR_156488.2:n.2186_2191del
  • p.Leu736_Asn737del
Links:
dbSNP: rs778896252
NCBI 1000 Genomes Browser:
rs778896252
Molecular consequence:
  • NM_000297.4:c.2208_2213del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NR_156488.2:n.2186_2191del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001481059Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely pathogenicunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not 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), SCV001481059.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The PKD2 p.Leu736_Asn737del variant was identified in 1 of 230 proband chromosomes (frequency: 0.004) from individuals or families with ADPKD and segregated with disease in multiple affected family members (Stekrova 2004). The variant was also identified in dbSNP (ID: rs778896252), LOVD 3.0 (2x ), and in ADPKD Mutation Database (as Highly Likely Pathogenic). The variant was not identified in ClinVar, or PKD1-LOVD. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). This variant is an in-frame deletion resulting in the removal of a Leucine (Leu) and Asparagine (Asn) residue at codon 736 and 737; the impact of this alteration on PKD2 protein function is not known. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 15, 2024