chr16-2091861-G-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001009944.3(PKD1):c.11457C>A(p.Tyr3819*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,330 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001009944.3 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.11457C>A | p.Tyr3819* | stop_gained | Exon 41 of 46 | ENST00000262304.9 | NP_001009944.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237682Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130396
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458330Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 725470
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Polycystic kidney disease, adult type Pathogenic:3
- -
Variant summary: PKD1 c.11457C>A (p.Tyr3819X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 4.2e-06 in 237682 control chromosomes. c.11457C>A has been reported in the literature in multiple individuals affected with Polycystic Kidney Disease 1 (e.g., Peral_1996). These data indicate that the variant is likely associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 9199561). ClinVar contains an entry for this variant (Variation ID: 8201). Based on the evidence outlined above, the variant was classified as pathogenic. -
- -
Autosomal dominant polycystic kidney disease Pathogenic:1
This sequence change in PKD1 is a nonsense variant predicted to cause a premature stop codon, p.(Tyr3819*), in biologically-relevant-exon 41/46 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (ClinGen). This variant is present in a single European (non-Finnish) individual in gnomAD v2.1 (1/104,690 alleles). The variant has been reported to segregate with polycystic kidney disease in at least two families (PMID: 19165178, 20950398). This variant has been identified as a de novo occurrence with confirmed parental relationships in an individual with polycystic kidney disease (PMID: 8845849). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PVS1, PS2, PP1_Moderate, PM2_Supporting. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at