PIK3AP1

phosphoinositide-3-kinase adaptor protein 1

Basic information

Region (hg38): 10:96593315-96720514

Links

ENSG00000155629 ∙ NCBI:118788 ∙ OMIM:607942 ∙ HGNC:30034 ∙ Uniprot:Q6ZUJ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Infantile_spasms (437 variants)
• not_specified (79 variants)
• not_provided (17 variants)
• PIK3AP1-related_disorder (13 variants)
• PIK3AP1-Associated_Seizure_Disorder (1 variants)
• PIK3AP1-related_early_onset_epileptic_encephalopathy (1 variants)

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. These statistics are base on transcript: NM_000152309.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	117	16	134
missense			236	17	5	258
nonsense			1			1
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	241	134	21

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIK3AP1	protein_coding	protein_coding	ENST00000339364	17	127203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000431	125731	0	2	125733	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	346	486	0.712	0.0000290	5274
Missense in Polyphen		112	191.23	0.58568		2046
Synonymous	1.54	172	200	0.861	0.0000135	1576
Loss of Function	5.64	1	39.0	0.0256	0.00000194	460

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	Medium	High

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