rs747483368
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_001009944.3(PKD1):c.2215C>T(p.Arg739Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 809,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R739Q) has been classified as Benign.
Frequency
Consequence
NM_001009944.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.2215C>T | p.Arg739Trp | missense_variant | 11/46 | ENST00000262304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.2215C>T | p.Arg739Trp | missense_variant | 11/46 | 1 | NM_001009944.3 | P5 | |
PKD1 | ENST00000423118.5 | c.2215C>T | p.Arg739Trp | missense_variant | 11/46 | 1 | A2 | ||
PKD1 | ENST00000488185.2 | c.472+2681C>T | intron_variant | 5 | |||||
PKD1 | ENST00000568591.5 | c.*543C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/12 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000124 AC: 1AN: 809142Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0AN XY: 415788
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Polycystic kidney disease;C0887850:Polycystic liver disease 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Polycystic kidney disease Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The PKD1 p.Gln739X variant was not identified in the literature nor was it identified in dbSNP, Clinvitae, ClinVar, GeneInsight-COGR, MutDB, ADPKD Mutation Database, PKD1-LOVD, and PKD1-LOVD 3.0. The p.Gln739X variant leads to a premature stop codon at position 739, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the PKD1 gene are an established mechanism of disease in autosomal dominant polycystic kidney disease and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at