CAB39

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

Basic information

Region (hg38): 2:230712841-230821075

Links

ENSG00000135932 ∙ NCBI:51719 ∙ OMIM:612174 ∙ HGNC:20292 ∙ Uniprot:Q9Y376 ∙ 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 CAB39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAB39 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in CAB39

This is a list of pathogenic ClinVar variants found in the CAB39 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-230790905-A-G		not specified	Uncertain significance (Feb 21, 2024)
2-230818541-C-T		not specified	Uncertain significance (Feb 06, 2024)
2-230818587-A-G		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAB39	protein_coding	protein_coding	ENST00000258418	8	108231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0680	0.929	125732	0	7	125739	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.38	86	175	0.493	0.00000867	2286
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000367	0.0000352
Middle Eastern	0.0000552	0.0000544
South Asian	0.0000455	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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;Neutrophil degranulation;Signal Transduction;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;Innate Immune System;Immune System;LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.693
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.653
• hipred: Y
• hipred_score: 0.798
• ghis: 0.572

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cab39

Gene ontology

• Biological process: cell cycle arrest;positive regulation of peptidyl-threonine phosphorylation;peptidyl-serine phosphorylation;signal transduction by protein phosphorylation;activation of protein kinase activity;intracellular signal transduction;neutrophil degranulation;protein heterooligomerization;cellular hypotonic response;positive regulation of protein serine/threonine kinase activity;negative regulation of potassium ion transmembrane transporter activity;negative regulation of potassium ion transmembrane transport
• Cellular component: extracellular region;cytosol;secretory granule lumen;extracellular exosome;serine/threonine protein kinase complex;ficolin-1-rich granule lumen
• Molecular function: protein serine/threonine kinase activity;protein binding;kinase binding;protein kinase activator activity;protein serine/threonine kinase activator activity