CAB39L

protein-coding

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

Gene summary

Predicted to enable protein serine/threonine kinase activator activity. Predicted to be involved in intracellular signal transduction. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001079670.3

Inheritance

—

ClinVar variants

U:43B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr13:49,308,650-49,444,064

External References & Databases

Ensembl (ENSG00000102547)

Transcript & Mutation Effects

hg38 • Region Span ~135.4 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 CAB39L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 42

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079670.3. 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			40 clinvar	1 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	43	2	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079670.3	RefSeq	NP_001073138.1	8	MANE Select
ENST00000409308.6	Ensembl	ENSP00000386375.1	8	MANE Select
NM_001287337.2	RefSeq	NP_001274266.1	8	Standard
NM_001287338.2	RefSeq	NP_001274267.1	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)
Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
Signal Transduction
Energy dependent regulation of mTOR by LKB1-AMPK

Biological Process

cell cycle arrest
signal transduction by protein phosphorylation

Molecular Function

protein serine/threonine kinase activity
protein binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355854
Coding exons: 8
Length: 135477
Individuals with no LoFs: 125620
Homozygous LoFs: 0
Heterozygous LoFs: 128
Defined: 125748
p: 0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.638	150	174	0.864	0.00000881	2238
Missense (PolyPhen)		53	65.683	0.8069		884
Synonymous	0.549	59	64.6	0.913	0.00000350	599
Loss of Function	1.56	9	15.7	0.575	7.23e-7	213

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.0022	0.0022	notable
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00089	0.00087	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

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 (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.915
RVIS EVS: -0.63
RVIS percentile EVS: 17.03

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.871

Gene Damage Prediction

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