PIK3AP1

phosphoinositide-3-kinase adaptor protein 1

Basic information

Region (hg38): 10:96593315-96720514

Links

ENSG00000155629NCBI:118788OMIM:607942HGNC:30034Uniprot:Q6ZUJ8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PIK3AP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3AP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
2
clinvar
103
clinvar
18
clinvar
123
missense
200
clinvar
10
clinvar
6
clinvar
216
nonsense
1
clinvar
1
start loss
0
frameshift
2
clinvar
2
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
11
11
2
24
non coding
1
clinvar
42
clinvar
2
clinvar
45
Total 0 0 209 155 26

Variants in PIK3AP1

This is a list of pathogenic ClinVar variants found in the PIK3AP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
10-96595608-G-C Infantile spasms Uncertain significance (Jul 19, 2023)1465817
10-96595608-G-T Infantile spasms Uncertain significance (Jun 27, 2022)1407144
10-96595616-G-A Infantile spasms Benign (Oct 08, 2023)474928
10-96595617-G-A Infantile spasms Uncertain significance (Dec 18, 2023)1360489
10-96595626-G-A Infantile spasms Uncertain significance (Jul 07, 2023)1385678
10-96595628-C-T Infantile spasms Likely benign (Aug 27, 2022)735437
10-96595629-G-A Infantile spasms Uncertain significance (Jan 30, 2024)1414381
10-96595651-G-T Infantile spasms Likely benign (Aug 23, 2022)1551922
10-96602261-A-C Infantile spasms Likely benign (Aug 17, 2023)2911997
10-96602261-A-G Infantile spasms Likely benign (Aug 06, 2022)1920256
10-96602261-A-T Infantile spasms Likely benign (Dec 11, 2023)1591470
10-96602265-C-A Infantile spasms Likely benign (Oct 23, 2022)2036613
10-96602266-A-G Infantile spasms Likely benign (Jul 06, 2022)1901500
10-96602274-T-C Infantile spasms Uncertain significance (Mar 15, 2020)1010512
10-96602286-G-A Infantile spasms Uncertain significance (Sep 08, 2021)847053
10-96602288-G-A Infantile spasms Likely benign (Dec 01, 2023)1084139
10-96602297-C-T Infantile spasms Benign (Jan 24, 2024)1170324
10-96602298-G-A Infantile spasms Uncertain significance (Oct 03, 2023)2889997
10-96602301-G-A Infantile spasms Uncertain significance (Sep 01, 2021)1063353
10-96602303-C-T Infantile spasms Benign (Jan 25, 2024)474927
10-96602305-C-G Infantile spasms Uncertain significance (Sep 13, 2022)1719366
10-96602305-C-T Infantile spasms • not specified Conflicting classifications of pathogenicity (Oct 16, 2023)707691
10-96602321-G-C Infantile spasms Likely benign (Mar 23, 2022)1159709
10-96602323-G-A Infantile spasms Uncertain significance (Sep 01, 2021)963571
10-96602329-T-C not specified Likely benign (Oct 06, 2022)2317280

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PIK3AP1protein_codingprotein_codingENST00000339364 17127203
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000431125731021257330.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.263464860.7120.00002905274
Missense in Polyphen112191.230.585682046
Synonymous1.541722000.8610.00001351576
Loss of Function5.64139.00.02560.00000194460

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008830.00000879
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Signaling adapter that contributes to B-cell development by linking B-cell receptor (BCR) signaling to the phosphoinositide 3-kinase (PI3K)-Akt signaling pathway. Has a complementary role to the BCR coreceptor CD19, coupling BCR and PI3K activation by providing a docking site for the PI3K subunit PIK3R1. Alternatively, links Toll-like receptor (TLR) signaling to PI3K activation, a process preventing excessive inflammatory cytokine production. Also involved in the activation of PI3K in natural killer cells. May be involved in the survival of mature B-cells via activation of REL. {ECO:0000269|PubMed:15893754}.;
Pathway
PI3K-Akt signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);B Cell Receptor Signaling Pathway;PI3K-Akt Signaling Pathway;Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;Disease;Signal Transduction;Signaling by the B Cell Receptor (BCR);TCR;Immune System;Adaptive Immune System;PIP3 activates AKT signaling;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;Intracellular signaling by second messengers;Diseases of signal transduction (Consensus)

Recessive Scores

pRec
0.107

Intolerance Scores

loftool
0.0355
rvis_EVS
0.05
rvis_percentile_EVS
57.48

Haploinsufficiency Scores

pHI
0.185
hipred
Y
hipred_score
0.825
ghis
0.493

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.298

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

Mouse Genome Informatics

Gene name
Pik3ap1
Phenotype
immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process
positive regulation of phosphatidylinositol 3-kinase signaling;toll-like receptor 2 signaling pathway;toll-like receptor 4 signaling pathway;toll-like receptor 7 signaling pathway;toll-like receptor 9 signaling pathway;phosphatidylinositol phosphorylation;regulation of inflammatory response;positive regulation of protein kinase B signaling
Cellular component
cytosol;plasma membrane;membrane
Molecular function
phosphatidylinositol 3-kinase regulatory subunit binding;identical protein binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity