CAB39

protein-coding

calcium binding protein 39, the group of Armadillo like helical domain containing

Gene summary

Enables protein serine/threonine kinase activator activity and protein serine/threonine kinase binding activity. Involved in cellular hypotonic response; intracellular signal transduction; and negative regulation of potassium ion transmembrane transport. Located in cytoplasm. Part of serine/threonine protein kinase complex. Implicated in hepatocellular carcinoma. Biomarker of hepatocellular carcinoma and pancreatic cancer. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016289.4

Inheritance

—

ClinVar variants

U:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr2:230,712,842-230,821,075

External References & Databases

Ensembl (ENSG00000135932)

Transcript & Mutation Effects

hg38 • Region Span ~108.2 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 CAB39 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016289.4. 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			1 clinvar			1
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	17	0	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016289.4	RefSeq	NP_057373.1	8	MANE Select
ENST00000258418.10	Ensembl	ENSP00000258418.5	8	MANE Select
NM_001130849.2	RefSeq	NP_001124321.1	8	Standard
NM_001130850.2	RefSeq	NP_001124322.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mTOR signaling pathway - Homo sapiens (human)
AMPK signaling pathway - Homo sapiens (human)
AMP-activated Protein Kinase (AMPK) Signaling
Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
Endochondral Ossification

Biological Process

cell cycle arrest
positive regulation of peptidyl-threonine phosphorylation
peptidyl-serine phosphorylation
signal transduction by protein phosphorylation
activation of protein kinase activity

Molecular Function

protein serine/threonine kinase activity
protein binding
kinase binding
protein kinase activator activity
protein serine/threonine kinase activator activity

Cellular Component

extracellular region
cytosol
secretory granule lumen
extracellular exosome
serine/threonine protein kinase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258418
Coding exons: 8
Length: 108231
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125739
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.38	86	175	0.493	0.00000867	2286
Missense (PolyPhen)		20	52.118	0.38374		757
Synonymous	1.17	54	66.1	0.816	0.00000390	589
Loss of Function	2.64	5	16.6	0.301	7.83e-7	227

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.000045	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of a complex that binds and activates STK11/LKB1. In the complex, required to stabilize the interaction between CAB39/MO25 (CAB39/MO25alpha or CAB39L/MO25beta) and STK11/LKB1. {ECO:0000269|PubMed:19892943}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.693
RVIS EVS: -0.05
RVIS percentile EVS: 49.76

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.903

Gene Damage Prediction

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