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NM_000297.4(PKD2):c.1081C>T (p.Arg361Ter) AND not provided

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Sep 1, 2023
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:
RCV000788690.30

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]
Observations:
1

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
SCV000927887Blueprint Genetics
criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)
Pathogenic
(Aug 28, 2018)
germlineclinical testing

Citation Link,

SCV001250327CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Apr 1, 2019)
germlineclinical testing

Citation Link,

SCV001782674GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Sep 1, 2023)
germlineclinical testing

Citation Link,

SCV003839866Genetic Services Laboratory, University of Chicago
no assertion criteria provided
Pathogenic
(Sep 2, 2022)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Blueprint Genetics, SCV000927887.1

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

From CeGaT Center for Human Genetics Tuebingen, SCV001250327.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV001782674.2

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30215095, 27782177, 30816285, 23376035, 25525159, 17100995, 22508176, 22863349, 31740684, 33168999, 33726816, 34101167, 33141305, 35478332)

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

From Genetic Services Laboratory, University of Chicago, SCV003839866.1

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

Description

DNA sequence analysis of the PKD2 gene demonstrated a sequence change, c.1081C>T, which results in the creation of a premature stop codon at amino acid position 361, p.Arg361*. This pathogenic sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated PKD2 protein with potentially abnormal function. This sequence change has not been described in population databases such as ExAC and gnomAD. This pathogenic sequence change has previously been described in multiple individuals with autosomal dominant polycystic kidney disease (PMID: 34101167, 30816285, 33141305, 31740684, 27782177, 17100995, 22508176). Based on these collective evidences, this sequence change is classified as pathogenic.

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

Last Updated: Oct 20, 2024