rs202017613
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_016529.6(ATP8A2):c.2333G>A(p.Arg778Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,613,636 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R778W) has been classified as Uncertain significance.
Frequency
Consequence
NM_016529.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP8A2 | NM_016529.6 | c.2333G>A | p.Arg778Gln | missense_variant | 25/37 | ENST00000381655.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP8A2 | ENST00000381655.7 | c.2333G>A | p.Arg778Gln | missense_variant | 25/37 | 1 | NM_016529.6 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152102Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000434 AC: 108AN: 248764Hom.: 1 AF XY: 0.000445 AC XY: 60AN XY: 134970
GnomAD4 exome AF: 0.000588 AC: 860AN: 1461416Hom.: 2 Cov.: 35 AF XY: 0.000605 AC XY: 440AN XY: 726974
GnomAD4 genome ? AF: 0.000401 AC: 61AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74432
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.2333G>A (p.R778Q) alteration is located in exon 25 (coding exon 25) of the ATP8A2 gene. This alteration results from a G to A substitution at nucleotide position 2333, causing the arginine (R) at amino acid position 778 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Cerebellar ataxia, intellectual disability, and dysequilibrium syndrome 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | May 03, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at