NM_000297.4(PKD2):c.2398A>C (p.Met800Leu) AND Joubert syndrome 7

Clinical significance:Benign

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001258257.1

Allele description [Variation Report for NM_000297.4(PKD2):c.2398A>C (p.Met800Leu)]

NM_000297.4(PKD2):c.2398A>C (p.Met800Leu)

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.2398A>C (p.Met800Leu)
HGVS:
  • NC_000004.12:g.88067937A>C
  • NG_008604.1:g.65270A>C
  • NM_000297.4:c.2398A>CMANE SELECT
  • NP_000288.1:p.Met800Leu
  • NC_000004.11:g.88989089A>C
  • NM_000297.3:c.2398A>C
  • NR_156488.2:n.2376A>C
  • Q13563:p.Met800Leu
Protein change:
M800L
Links:
UniProtKB: Q13563#VAR_058829; dbSNP: rs2234917
NCBI 1000 Genomes Browser:
rs2234917
Molecular consequence:
  • NM_000297.4:c.2398A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_156488.2:n.2376A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Joubert syndrome 7 (JBTS7)
Identifiers:
MONDO: MONDO:0012694; MedGen: C1969053; Orphanet: 220497; OMIM: 611560

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001435171Broad Institute Rare Disease Group, Broad Institutecriteria provided, single submitter
Benigngermlineresearch

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

[Genetic analysis (PKD2) of autosomal dominant polycystic kidney disease].

Gómez PF, Moro EC, García-Cosmes P, Sarmiento RG, Romo JM.

Nefrologia. 2009;29(6):562-8. doi: 10.3265/Nefrologia.2009.29.6.5511.en.full. Spanish.

PubMed [citation]
PMID:
19936001

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 Broad Institute Rare Disease Group, Broad Institute, SCV001435171.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)

Description

The heterozygous p.Met800Leu variant in PKD2 has been identified in 3 individuals with polycystic kidney disease, segregated with disease in 3 individuals from 1 family (PMID: 19936001), and has been identified in >1% of South Asian chromosomes and 4 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for autosomal dominant polycystic kidney disease.

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

Last Updated: Jun 23, 2021

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