NM_001009944.3(PKD1):c.9561CAA[1] (p.Asn3188del) AND Inborn genetic diseases

Clinical significance:Pathogenic (Last evaluated: Aug 7, 2013)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001009944.3(PKD1):c.9561CAA[1] (p.Asn3188del)]

NM_001009944.3(PKD1):c.9561CAA[1] (p.Asn3188del)

PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_001009944.3(PKD1):c.9561CAA[1] (p.Asn3188del)
  • NC_000016.10:g.2100399TGT[1]
  • NG_008617.1:g.42818CAA[1]
  • NM_000296.4:c.9561CAA[1]
  • NM_001009944.3:c.9561CAA[1]MANE SELECT
  • NP_000287.4:p.Asn3188del
  • NP_001009944.3:p.Asn3188del
  • NC_000016.9:g.2150400TGT[1]
  • NM_000296.3:c.9564_9566del
  • NM_001009944.2:c.9564_9566del
Protein change:
dbSNP: rs869312944
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000296.4:c.9561CAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001009944.3:c.9561CAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]


Inborn genetic diseases
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000262953Ambry Geneticscriteria provided, single submitter
(Aug 7, 2013)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV000262953.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided


The c.9564_9566delCAA (p.N3188del) alteration is located in coding exon 27 of the PKD1gene. This alteration results from an in-frame deletion from nucleotide position 9564 through 9566, resulting in the deletion of asperagine at codon 3188. The alteration is not observed in healthy cohorts:Based on data from the NHLBI Exome Sequencing Project (ESP), the PKD1 c.9564_9566delCAA (p.N3188del) alteration was not observed among 6,498 individuals tested (0.0%). Allele frequency data for this nucleotide position is not currently available from the 1000 Genomes Project and the alteration is not currently listed in the Database of Single Nucleotide Polymorphisms (dbSNP). The altered amino acid is conserved throughout evolution:The p.N3188 amino acid is conserved throughout vertebrates. The amino acid is located in a functionally important protein domain:The c.9564_9566delCAA (p.N3188del) alteration is located within the fhe first cytoplasmic loop in the transmembrane region of the PKD1 gene, a region which is among the highest regions of conservation in the gene (Stanford et al., 1997).The amino acid change has been observed in affected individuals:This alteration has been described in the literature (see below for details) and is observed in the HGMD database (CD034171). The alteration was identifed in a female proband with ADPKD renal findings in addition to a vascular phenotype which was described as a ruptured intracranial aneurysm at the age of 31 (Rosetti et al., 2003).The alteration has cosegregated with disease:This PKD1 alteration was detected in our laboratory via exome sequencing in a patient with ADPKD (12-64954). The alteration co-segregated with the disease, as the affected father (12-64956) also manifested the alteration.Based on the available evidence, the PKD1 c.9564_9566delCAA (p.N3188del) alteration is classified as a pathogenic mutation.Rosetti S, et al. (2003) Lancet 361:2196-2201.Stanford R, et al. (1997) Hum Mol Genet 6(9):1483–1489.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2021

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