3-193514820-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_032279.4(ATP13A4):c.112G>A(p.Gly38Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000285 in 1,614,032 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 (★).
Frequency
Consequence
NM_032279.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP13A4 | NM_032279.4 | c.112G>A | p.Gly38Arg | missense_variant | Exon 2 of 30 | ENST00000342695.9 | NP_115655.2 | |
ATP13A4 | XM_047449063.1 | c.241G>A | p.Gly81Arg | missense_variant | Exon 4 of 32 | XP_047305019.1 | ||
ATP13A4 | XM_017007319.2 | c.241G>A | p.Gly81Arg | missense_variant | Exon 4 of 27 | XP_016862808.2 | ||
ATP13A4 | XR_007095757.1 | n.505G>A | non_coding_transcript_exon_variant | Exon 4 of 26 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251376Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135866
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.112G>A (p.G38R) alteration is located in exon 2 (coding exon 2) of the ATP13A4 gene. This alteration results from a G to A substitution at nucleotide position 112, causing the glycine (G) at amino acid position 38 to be replaced by an arginine (R). 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