chr10-96602298-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152309.3(PIK3AP1):c.2342C>T(p.Pro781Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000311 in 1,605,546 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P781P) has been classified as Benign.
Frequency
Consequence
NM_152309.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2342C>T | p.Pro781Leu | missense_variant | 16/17 | ENST00000339364.10 | |
LOC105378443 | XR_946220.4 | n.1447-5378G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2342C>T | p.Pro781Leu | missense_variant | 16/17 | 1 | NM_152309.3 | P1 | |
PIK3AP1 | ENST00000371109.3 | c.1139C>T | p.Pro380Leu | missense_variant | 9/10 | 1 | |||
PIK3AP1 | ENST00000371110.6 | c.1808C>T | p.Pro603Leu | missense_variant | 15/16 | 2 | |||
PIK3AP1 | ENST00000467625.5 | n.539C>T | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1453406Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 723138
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
Infantile spasms Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 781 of the PIK3AP1 protein (p.Pro781Leu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PIK3AP1-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at