NM_006045.3:c.2276G>A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_006045.3(ATP9A):c.2276G>A(p.Arg759Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006045.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP9A | ENST00000338821.6 | c.2276G>A | p.Arg759Gln | missense_variant | Exon 21 of 28 | 1 | NM_006045.3 | ENSP00000342481.5 | ||
ATP9A | ENST00000311637.9 | c.1868G>A | p.Arg623Gln | missense_variant | Exon 16 of 23 | 1 | ENSP00000309086.5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1459708Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 6AN XY: 726150
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74298
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2276G>A (p.R759Q) alteration is located in exon 21 (coding exon 21) of the ATP9A gene. This alteration results from a G to A substitution at nucleotide position 2276, causing the arginine (R) at amino acid position 759 to be replaced by a glutamine (Q). 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