NM_001009944.3(PKD1):c.5847C>T (p.Ser1949=) AND Polycystic kidney dysplasia

Clinical significance:Benign

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001292412.1

Allele description [Variation Report for NM_001009944.3(PKD1):c.5847C>T (p.Ser1949=)]

NM_001009944.3(PKD1):c.5847C>T (p.Ser1949=)

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.5847C>T (p.Ser1949=)
HGVS:
  • NC_000016.10:g.2109320G>A
  • NG_008617.1:g.31579C>T
  • NM_000296.4:c.5847C>T
  • NM_001009944.3:c.5847C>TMANE SELECT
  • NP_000287.4:p.Ser1949=
  • NP_001009944.3:p.Ser1949=
  • NC_000016.9:g.2159321G>A
  • NM_000296.3:c.5847C>T
  • NM_001009944.2:c.5847C>T
  • p.Ser1949Ser
Links:
dbSNP: rs80111665
NCBI 1000 Genomes Browser:
rs80111665
Molecular consequence:
  • NM_000296.4:c.5847C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001009944.3:c.5847C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Polycystic kidney dysplasia
Synonyms:
Polycystic kidney disease
Identifiers:
MONDO: MONDO:0020642; MedGen: C0022680; OMIM: PS173900; Human Phenotype Ontology: HP:0000113

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001480841Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedBenignunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001480841.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The PKD1 p.Ser1949= variant was identified in 1 of 460 proband chromosomes (frequency: 0.002) from individuals or families with ADPKD, and was present in 1 of 92 control chromosomes (frequency: 0.01) from healthy individuals (Rossetti_2012_22383692, Phakdeekitcharoen_2000_11012875). The variant was also identified in dbSNP (ID: rs80111665) as “With Likely benign allele”, ClinVar (classified as benign by ARUP Laboratories and likely benign by PreventionGenetics), and the ADPKD Mutation Database (classified as likely neutral). The variant was not identified in GeneInsight-COGR, LOVD 3.0, or PKD1-LOVD databases. The variant was identified in control databases in 1665 of 257370 chromosomes (38 homozygous) at a frequency of 0.006 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 3 of 22624 chromosomes (freq: 0.0001), Other in 41 of 6190 chromosomes (freq: 0.007), Latino in 112 of 33994 chromosomes (freq: 0.003), European Non-Finnish in 123 of 119088 chromosomes (freq: 0.001), Ashkenazi Jewish in 53 of 9568 chromosomes (freq: 0.006), East Asian in 1005 of 18588 chromosomes (freq: 0.05), European Finnish in 280 of 17560 chromosomes (freq: 0.02), and South Asian in 48 of 29758 chromosomes (freq: 0.002). In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. The p.Ser1949= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In summary, based on the above information this variant meets our laboratory criteria to be classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 20, 2021

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