CAB39L

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

Basic information

Region (hg38): 13:49308650-49444064

Links

ENSG00000102547 ∙ NCBI:81617 ∙ OMIM:612175 ∙ HGNC:20290 ∙ Uniprot:Q9H9S4 ∙ 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 CAB39L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAB39L 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in CAB39L

This is a list of pathogenic ClinVar variants found in the CAB39L region.

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

Position	Type	Phenotype	Significance	ClinVar
13-49310824-G-A		not specified	Uncertain significance (Sep 26, 2024)
13-49310834-A-C		not specified	Uncertain significance (Dec 19, 2023)
13-49310857-T-C		not specified	Uncertain significance (Oct 14, 2023)
13-49310873-C-T		not specified	Likely benign (Aug 13, 2021)
13-49310901-T-G		not specified	Uncertain significance (May 15, 2024)
13-49310923-A-G		not specified	Uncertain significance (Sep 03, 2024)
13-49310957-C-T		not specified	Uncertain significance (Jun 10, 2024)
13-49332009-T-A		not specified	Uncertain significance (Sep 28, 2022)
13-49332042-T-C		not specified	Uncertain significance (Dec 09, 2023)
13-49332051-T-C		not specified	Uncertain significance (Jun 17, 2022)
13-49332072-G-C		not specified	Uncertain significance (Dec 10, 2024)
13-49339697-T-C		not specified	Uncertain significance (Aug 01, 2024)
13-49350856-C-T		not specified	Uncertain significance (Mar 12, 2024)
13-49350886-C-T		not specified	Uncertain significance (Oct 26, 2021)
13-49350912-T-C		not specified	Likely benign (Jul 25, 2024)
13-49359745-G-C		not specified	Uncertain significance (Jun 07, 2023)
13-49359754-T-C		not specified	Uncertain significance (Dec 30, 2023)
13-49359771-C-A		not specified	Uncertain significance (Oct 29, 2024)
13-49359778-T-C		not specified	Uncertain significance (Aug 15, 2024)
13-49376983-T-C		not specified	Uncertain significance (Jun 27, 2022)
13-49376990-C-A		not specified	Uncertain significance (Dec 20, 2023)
13-49377005-C-A		not specified	Uncertain significance (Nov 27, 2024)
13-49377010-A-C		not specified	Uncertain significance (Oct 26, 2021)
13-49377011-G-C		not specified	Uncertain significance (Oct 26, 2021)
13-49377058-G-A		not specified	Uncertain significance (Nov 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAB39L	protein_coding	protein_coding	ENST00000355854	8	135477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000639	0.909	125620	0	128	125748	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.638	150	174	0.864	0.00000881	2238
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00224	0.00224
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.000889	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000889	0.000870
South Asian	0.000132	0.000131
Other	0.000165	0.000163

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 (By similarity). {ECO:0000250}.
• Pathway: 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;mTOR signalling (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.915
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.428
• hipred: Y
• hipred_score: 0.713
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cab39l
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: cell cycle arrest;signal transduction by protein phosphorylation
• Cellular component: cytosol
• Molecular function: protein serine/threonine kinase activity;protein binding