rs201383632
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_000278.5(PAX2):c.478G>A(p.Ala160Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000101 in 1,589,888 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000278.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000134 AC: 28AN: 208830Hom.: 0 AF XY: 0.000126 AC XY: 14AN XY: 111494
GnomAD4 exome AF: 0.000105 AC: 151AN: 1437610Hom.: 1 Cov.: 31 AF XY: 0.000105 AC XY: 75AN XY: 712376
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74456
ClinVar
Submissions by phenotype
not provided Uncertain:2
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Renal coloboma syndrome;C4014925:Focal segmental glomerulosclerosis 7 Uncertain:1
This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 160 of the PAX2 protein (p.Ala160Thr). This variant is present in population databases (rs201383632, gnomAD 0.03%). This missense change has been observed in individual(s) with renal coloboma syndrome and was also identified in the individual's unaffected mother (PMID: 22213154). ClinVar contains an entry for this variant (Variation ID: 569063). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at