STK11IP

protein-coding

serine/threonine kinase 11 interacting protein

Gene summary

Enables protein kinase binding activity. Involved in intracellular protein localization. Located in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_052902.4

Inheritance

—

ClinVar variants

U:199B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr2:219,597,857-219,616,451

External References & Databases

Ensembl (ENSG00000144589)

Transcript & Mutation Effects

hg38 • Region Span ~18.6 kb

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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 STK11IP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 202

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052902.4. 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			5 clinvar			5
missense			187 clinvar	20 clinvar		207
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	199	20	0	219

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052902.4	RefSeq	NP_443134.3	24	MANE Select
ENST00000456909.6	Ensembl	ENSP00000389383.1	24	MANE Select
ENST00000413891.5	Ensembl	ENSP00000403923.1	5	Standard
ENST00000447191.1	Ensembl	ENSP00000406371.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System
TGF_beta_Receptor
LKB1 signaling events

Biological Process

cytoskeleton organization
protein localization
neutrophil degranulation

Molecular Function

protein kinase binding

Cellular Component

extracellular region
cytoplasm
lysosomal membrane
azurophil granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295641
Coding exons: 25
Length: 18592
Individuals with no LoFs: 124994
Homozygous LoFs: 0
Heterozygous LoFs: 222
Defined: 125216
p: 0.000887

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.509	604	640	0.943	0.0000391	6917
Missense (PolyPhen)		220	253.06	0.86935		2965
Synonymous	0.708	251	266	0.945	0.0000149	2362
Loss of Function	2.46	40	60.7	0.659	0.00000356	621

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00096	0.00088	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.0087	0.0081	notable
East Asian	0.00082	0.00077	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00067	0.00061	rare
South Asian	0.00072	0.00072	rare
Other	0.0018	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate STK11/LKB1 function by controlling its subcellular localization. {ECO:0000269|PubMed:11741830}.;

Recessive Scores

pRec: 0.0895

Intolerance Scores

RVIS EVS: -0.21
RVIS percentile EVS: 37.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.743

Gene Damage Prediction

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