chr4-88074903-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PP3_ModerateBS2
The NM_000297.4(PKD2):āc.2614C>Gā(p.Arg872Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,922 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 Uncertain significance (ā ā ).
Frequency
Consequence
NM_000297.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251096Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135672
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461840Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727224
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
Autosomal dominant polycystic kidney disease Uncertain:1
This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 872 of the PKD2 protein (p.Arg872Gly). This variant is present in population databases (rs755226061, gnomAD 0.009%). This missense change has been observed in individual(s) with clinical features of polycystic kidney disease (PMID: 23300259, 32457805). ClinVar contains an entry for this variant (Variation ID: 1060358). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt PKD2 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Polycystic kidney disease 2 Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at