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NM_000297.4(PKD2):c.2208_2213del (p.Leu736_Asn737del) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Apr 12, 2022
Review status:
criteria provided, conflicting classifications
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:
RCV000756537.12

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]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000884372ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)
Likely pathogenic
(May 31, 2017)
germlineclinical testing

Citation Link,

SCV000920753Gharavi Laboratory, Columbia University
no assertion criteria provided

(ACMG Guidelines, 2015)
Uncertain significance
(Sep 16, 2018)
germlineresearch

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

SCV002504002GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Apr 12, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedresearch

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884372.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Gharavi Laboratory, Columbia University, SCV000920753.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV002504002.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Identified in an individual with end stage renal disease and liver cysts and her daughter with renal cysts and normal renal function in published literature (Stekrova et al., 2004); In-frame deletion of 2 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27071085, 31589614, 14993477)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024