3-193514846-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032279.4(ATP13A4):c.86G>T(p.Gly29Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,026 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP13A4 | NM_032279.4 | c.86G>T | p.Gly29Val | missense_variant | 2/30 | ENST00000342695.9 | NP_115655.2 | |
ATP13A4 | XM_047449063.1 | c.215G>T | p.Gly72Val | missense_variant | 4/32 | XP_047305019.1 | ||
ATP13A4 | XM_017007319.2 | c.215G>T | p.Gly72Val | missense_variant | 4/27 | XP_016862808.2 | ||
ATP13A4 | XR_007095757.1 | n.479G>T | non_coding_transcript_exon_variant | 4/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP13A4 | ENST00000342695.9 | c.86G>T | p.Gly29Val | missense_variant | 2/30 | 1 | NM_032279.4 | ENSP00000339182 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251378Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135880
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461870Hom.: 1 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.86G>T (p.G29V) alteration is located in exon 2 (coding exon 2) of the ATP13A4 gene. This alteration results from a G to T substitution at nucleotide position 86, causing the glycine (G) at amino acid position 29 to be replaced by a valine (V). 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