rs1555453872

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The ENST00000262304.9(PKD1):​c.6994_7000del​(p.Ala2332TrpfsTer7) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (β˜…β˜…). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PKD1
ENST00000262304.9 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:6

Conservation

PhyloP100: 5.36
Variant links:
Genes affected
PKD1 (HGNC:9008): (polycystin 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 16-2107947-ACGCCAGC-A is Pathogenic according to our data. Variant chr16-2107947-ACGCCAGC-A is described in ClinVar as [Pathogenic]. Clinvar id is 972870.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2107947-ACGCCAGC-A is described in Lovd as [Pathogenic]. Variant chr16-2107947-ACGCCAGC-A is described in Lovd as [Pathogenic]. Variant chr16-2107947-ACGCCAGC-A is described in Lovd as [Pathogenic]. Variant chr16-2107947-ACGCCAGC-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PKD1NM_001009944.3 linkuse as main transcriptc.6994_7000del p.Ala2332TrpfsTer7 frameshift_variant 16/46 ENST00000262304.9 NP_001009944.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PKD1ENST00000262304.9 linkuse as main transcriptc.6994_7000del p.Ala2332TrpfsTer7 frameshift_variant 16/461 NM_001009944.3 ENSP00000262304 P5P98161-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
7.17e-7
AC:
1
AN:
1394114
Hom.:
0
AF XY:
0.00000145
AC XY:
1
AN XY:
687768
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.27e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingGeneDxMay 21, 2024Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32823016, 11012875, 31740684, 29633482, 22508176, 33437033, 11115377) -
Pathogenic, criteria provided, single submitterclinical testingMolecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical ResearchJan 01, 2019- -
Pathogenic, criteria provided, single submitterclinical testingAthena DiagnosticsApr 05, 2021This variant is expected to result in the loss of a functional protein. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant has been identified in at least one individual with clinical features associated with this gene. -
Polycystic kidney disease, adult type Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingJuno Genomics, Hangzhou Juno Genomics, IncJul 19, 2024PM2_Supporting+PVS1+PS4_Supporting+PP4 -
Pathogenic, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsApr 09, 2022- -
PKD1-related disorder Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 13, 2024The PKD1 c.6994_7000del7 variant is predicted to result in a frameshift and premature protein termination (p.Ala2332Trpfs*7). This variant has been reported to be pathogenic for autosomal dominant polycystic kidney disease (ADPKD) (see for example, Phakdeekitcharoen et al. 2000. PubMed ID: 11012875; Table S3 of Mallawaarachchi et al. 2021. PubMed ID: 33437033). This variant has not been reported in a large population database, indicating this variant is rare. Frameshift variants in PKD1 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555453872; hg19: chr16-2157948; API