rs745748841
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005765.3(ATP6AP2):c.315T>A(p.Ser105Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,203,340 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_005765.3 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 | UniProt |
---|---|---|---|---|---|---|---|
ATP6AP2 | NM_005765.3 | c.315T>A | p.Ser105Arg | missense_variant | 4/9 | ENST00000636580.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6AP2 | ENST00000636580.2 | c.315T>A | p.Ser105Arg | missense_variant | 4/9 | 1 | NM_005765.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000888 AC: 1AN: 112604Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34752
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1090736Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 357444
GnomAD4 genome ? AF: 0.00000888 AC: 1AN: 112604Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34752
ClinVar
Submissions by phenotype
Syndromic X-linked intellectual disability Hedera type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 04, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with ATP6AP2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 105 of the ATP6AP2 protein (p.Ser105Arg). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at