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NM_000297.4(PKD2):c.390C>A (p.Ala130=) AND Autosomal dominant polycystic kidney disease

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 7, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001903645.4

Allele description [Variation Report for NM_000297.4(PKD2):c.390C>A (p.Ala130=)]

NM_000297.4(PKD2):c.390C>A (p.Ala130=)

Genes:
LOC129992813:ATAC-STARR-seq lymphoblastoid silent region 15559 [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.390C>A (p.Ala130=)
HGVS:
  • NC_000004.12:g.88008123C>A
  • NG_008604.1:g.5456C>A
  • NM_000297.4:c.390C>AMANE SELECT
  • NP_000288.1:p.Ala130=
  • NC_000004.11:g.88929275C>A
  • NR_156488.2:n.489C>A
Links:
dbSNP: rs1249701986
NCBI 1000 Genomes Browser:
rs1249701986
Molecular consequence:
  • NR_156488.2:n.489C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000297.4:c.390C>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Autosomal dominant polycystic kidney disease (ADPKD)
Identifiers:
MONDO: MONDO:0004691; MedGen: C0085413

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002170175Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 7, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002170175.3

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

Description

This sequence change affects codon 130 of the PKD2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PKD2 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with PKD2-related conditions.

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

Last Updated: Sep 29, 2024