rs146132289
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_033419.5(PGAP3):c.209A>T(p.Tyr70Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000818 in 1,613,196 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_033419.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152170Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251400Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135878
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1460908Hom.: 1 Cov.: 31 AF XY: 0.0000908 AC XY: 66AN XY: 726714
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152288Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74464
ClinVar
Submissions by phenotype
Hyperphosphatasia with intellectual disability syndrome 4 Uncertain:1
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Inborn genetic diseases Uncertain:1
The c.209A>T (p.Y70F) alteration is located in exon 2 (coding exon 2) of the PGAP3 gene. This alteration results from a A to T substitution at nucleotide position 209, causing the tyrosine (Y) at amino acid position 70 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at