PIK3IP1

phosphoinositide-3-kinase interacting protein 1

Basic information

Region (hg38): 22:31281594-31292534

Links

ENSG00000100100 ∙ NCBI:113791 ∙ OMIM:619158 ∙ HGNC:24942 ∙ Uniprot:Q96FE7 ∙ 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 PIK3IP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3IP1 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in PIK3IP1

This is a list of pathogenic ClinVar variants found in the PIK3IP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-31283109-C-T		not specified	Uncertain significance (Dec 27, 2023)
22-31283116-G-A		not specified	Uncertain significance (Oct 02, 2023)
22-31283128-C-T		not specified	Uncertain significance (Nov 17, 2023)
22-31283131-C-T		not specified	Uncertain significance (Mar 15, 2024)
22-31283138-G-T		not specified	Uncertain significance (Oct 30, 2024)
22-31283187-A-G		not specified	Uncertain significance (Jan 16, 2024)
22-31283190-T-C		not specified	Uncertain significance (Aug 22, 2023)
22-31283238-A-G		not specified	Uncertain significance (Dec 26, 2023)
22-31283281-C-T		not specified	Uncertain significance (Oct 11, 2024)
22-31289544-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
22-31289550-T-G		not specified	Uncertain significance (Feb 27, 2025)
22-31289551-G-C		not specified	Uncertain significance (Jul 30, 2024)
22-31289588-C-A		not specified	Uncertain significance (Feb 21, 2025)
22-31291037-C-T		not specified	Uncertain significance (Apr 12, 2022)
22-31291082-C-T		not specified	Uncertain significance (Dec 20, 2023)
22-31291186-C-G		not specified	Uncertain significance (Nov 08, 2021)
22-31291186-C-T		not specified	Uncertain significance (Oct 12, 2024)
22-31292302-G-T		not specified	Uncertain significance (Apr 09, 2024)
22-31292309-G-T		not specified	Uncertain significance (Sep 16, 2021)
22-31292310-C-T		not specified	Uncertain significance (Oct 14, 2021)
22-31292320-A-G		not specified	Uncertain significance (Sep 22, 2023)
22-31292331-C-A		not specified	Uncertain significance (Oct 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIK3IP1	protein_coding	protein_coding	ENST00000215912	6	10942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0151	0.961	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.873	112	141	0.793	0.00000708	1662
Missense in Polyphen		28	42.862	0.65326		525
Synonymous	-0.189	62	60.1	1.03	0.00000338	531
Loss of Function	1.96	5	12.5	0.400	6.19e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000499	0.0000462
European (Non-Finnish)	0.0000548	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of hepatic phosphatidylinositol 3- kinase (PI3K) activity. {ECO:0000250}.
• Pathway: Focal Adhesion-PI3K-Akt-mTOR-signaling pathway (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.351
• hipred: N
• hipred_score: 0.231
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pik3ip1

Gene ontology

• Biological process: negative regulation of phosphatidylinositol 3-kinase signaling;negative regulation of phosphatidylinositol 3-kinase activity
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;phosphatidylinositol 3-kinase catalytic subunit binding