rs138090835
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The ENST00000377346.9(PIK3CD):c.1802G>A(p.Arg601Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,613,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R601W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000377346.9 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 |
---|---|---|---|---|---|---|---|---|
PIK3CD | NM_005026.5 | c.1802G>A | p.Arg601Gln | missense_variant | 14/24 | ENST00000377346.9 | NP_005017.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3CD | ENST00000377346.9 | c.1802G>A | p.Arg601Gln | missense_variant | 14/24 | 1 | NM_005026.5 | ENSP00000366563 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250968Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135832
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461096Hom.: 0 Cov.: 35 AF XY: 0.0000426 AC XY: 31AN XY: 726892
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74346
ClinVar
Submissions by phenotype
Immunodeficiency 14 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 27, 2023 | 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. This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 601 of the PIK3CD protein (p.Arg601Gln). This variant is present in population databases (rs138090835, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with PIK3CD-related conditions. ClinVar contains an entry for this variant (Variation ID: 575784). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PIK3CD protein function. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at