PIK3IP1

protein-coding

phosphoinositide-3-kinase interacting protein 1

Gene summary

Enables phosphatidylinositol 3-kinase inhibitor activity. Involved in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction. Predicted to be located in plasma membrane. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_052880.5

Inheritance

—

ClinVar variants

U:47B:1

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr22:31,281,594-31,292,534

External References & Databases

Ensembl (ENSG00000100100)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PIK3IP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052880.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			44 clinvar	1 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	1	0	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052880.5	RefSeq	NP_443112.2	6	MANE Select
ENST00000215912.10	Ensembl	ENSP00000215912.4	6	MANE Select
NM_001135911.1	RefSeq	NP_001129383.1	5	Standard
ENST00000402249.7	Ensembl	ENSP00000385204.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Focal Adhesion-PI3K-Akt-mTOR-signaling pathway

Biological Process

negative regulation of phosphatidylinositol 3-kinase signaling
negative regulation of phosphatidylinositol 3-kinase activity

Molecular Function

protein binding
phosphatidylinositol 3-kinase catalytic subunit binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000215912
Coding exons: 6
Length: 10942
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125747
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.873	112	141	0.793	0.00000708	1662
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Negative regulator of hepatic phosphatidylinositol 3- kinase (PI3K) activity. {ECO:0000250}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.534
RVIS EVS: 0.35
RVIS percentile EVS: 74.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.111

Gene Damage Prediction

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