NM_001009944.3(PKD1):c.7300C>T (p.Arg2434Trp) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1);Pathogenic(1);Uncertain significance(1) (Last evaluated: May 8, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV001172091.5

Allele description [Variation Report for NM_001009944.3(PKD1):c.7300C>T (p.Arg2434Trp)]

NM_001009944.3(PKD1):c.7300C>T (p.Arg2434Trp)

Gene:
PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001009944.3(PKD1):c.7300C>T (p.Arg2434Trp)
HGVS:
  • NC_000016.10:g.2106587G>A
  • NG_008617.1:g.34312C>T
  • NM_000296.4:c.7300C>T
  • NM_001009944.3:c.7300C>TMANE SELECT
  • NP_000287.4:p.Arg2434Trp
  • NP_001009944.3:p.Arg2434Trp
  • NC_000016.9:g.2156588G>A
  • NM_000296.3:c.7300C>T
  • NM_001009944.2:c.7300C>T
  • p.R2434W
Protein change:
R2434W
Links:
dbSNP: rs151257298
NCBI 1000 Genomes Browser:
rs151257298
Molecular consequence:
  • NM_000296.4:c.7300C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001009944.3:c.7300C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001335034CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Mar 1, 2020)
germlineclinical testing

Citation Link,

SCV001475263Athena Diagnostics Inccriteria provided, single submitter
Likely pathogenic
(Dec 9, 2019)
unknownclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV001794327GeneDxcriteria provided, single submitter
Uncertain significance
(May 8, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Type of PKD1 mutation influences renal outcome in ADPKD.

Cornec-Le Gall E, Audrézet MP, Chen JM, Hourmant M, Morin MP, Perrichot R, Charasse C, Whebe B, Renaudineau E, Jousset P, Guillodo MP, Grall-Jezequel A, Saliou P, Férec C, Le Meur Y.

J Am Soc Nephrol. 2013 May;24(6):1006-13. doi: 10.1681/ASN.2012070650. Epub 2013 Feb 21.

PubMed [citation]
PMID:
23431072
PMCID:
PMC3665389

Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing.

Rossetti S, Hopp K, Sikkink RA, Sundsbak JL, Lee YK, Kubly V, Eckloff BW, Ward CJ, Winearls CG, Torres VE, Harris PC.

J Am Soc Nephrol. 2012 May;23(5):915-33. doi: 10.1681/ASN.2011101032. Epub 2012 Mar 1.

PubMed [citation]
PMID:
22383692
PMCID:
PMC3338301
See all PubMed Citations (6)

Details of each submission

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001335034.5

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

From Athena Diagnostics Inc, SCV001475263.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

The frequency of this variant in the general population is consistent with pathogenicity. Predicted to have a damaging effect on the protein. Located in potentially critical domain of the protein. Found in multiple individuals with expected phenotype for this gene. Occurs in a single case with an alternate molecular basis for disease. One de novo case with parental identity not confirmed.

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

From GeneDx, SCV001794327.1

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

Description

Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31056860, 31740684, 29338003, 22508176, 22383692, 23431072, 21115670)

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

Last Updated: Nov 27, 2021

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