CBLL1

Cbl proto-oncogene like 1, the group of Ring finger proteins|WTAP complex

Basic information

Region (hg38): 7:107743073-107761667

Links

ENSG00000105879 ∙ NCBI:79872 ∙ OMIM:606872 ∙ HGNC:21225 ∙ Uniprot:Q75N03 ∙ 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 CBLL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLL1 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CBLL1

This is a list of pathogenic ClinVar variants found in the CBLL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-107744167-G-A		not specified	Uncertain significance (Dec 07, 2024)
7-107748979-C-T		not specified	Uncertain significance (Sep 12, 2023)
7-107748988-C-T		not specified	Uncertain significance (Nov 25, 2024)
7-107749002-A-G		not specified	Uncertain significance (Oct 05, 2023)
7-107749020-C-T		not specified	Uncertain significance (Jun 03, 2024)
7-107749039-G-A		not specified	Uncertain significance (Dec 14, 2023)
7-107753925-C-G		not specified	Uncertain significance (Dec 20, 2023)
7-107755460-C-T		not specified	Uncertain significance (Nov 19, 2024)
7-107758346-A-C		not specified	Uncertain significance (Dec 16, 2024)
7-107758484-G-A		not specified	Uncertain significance (Mar 17, 2023)
7-107758505-C-G		not specified	Uncertain significance (Oct 18, 2021)
7-107758586-T-C		not specified	Uncertain significance (Nov 06, 2024)
7-107758831-A-G		not specified	Uncertain significance (Sep 20, 2024)
7-107758865-C-T		not specified	Uncertain significance (Mar 01, 2025)
7-107758915-G-A		not specified	Uncertain significance (Jan 19, 2025)
7-107758925-C-G		not specified	Uncertain significance (Jul 19, 2023)
7-107758925-C-T		not specified	Uncertain significance (Jul 09, 2021)
7-107758952-C-G		not specified	Uncertain significance (Jun 13, 2024)
7-107758958-C-A		not specified	Uncertain significance (Feb 08, 2025)
7-107758976-A-T		not specified	Uncertain significance (Jan 23, 2024)
7-107759128-C-T		not specified	Uncertain significance (Jan 19, 2025)
7-107759162-G-A		not specified	Uncertain significance (Oct 18, 2021)
7-107759163-A-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBLL1	protein_coding	protein_coding	ENST00000440859	6	17971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000822	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	222	286	0.777	0.0000147	3228
Missense in Polyphen		50	97.642	0.51208		1122
Synonymous	-1.56	109	90.1	1.21	0.00000464	975
Loss of Function	4.20	0	20.5	0.00	0.00000141	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of several tyrosine-phosphorylated Src substrates, including CDH1, CTTN and DOK1 (By similarity). Targets CDH1 for endocytosis and degradation (By similarity). Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Its function in the WMM complex is unknown (PubMed:29507755). {ECO:0000250|UniProtKB:Q9JIY2, ECO:0000269|PubMed:29507755}.
• Pathway: Disease;Infectious disease;Posttranslational regulation of adherens junction stability and dissassembly;InlA-mediated entry of Listeria monocytogenes into host cells;Listeria monocytogenes entry into host cells (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.788
• ghis: 0.664

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbll1

Gene ontology

• Biological process: negative regulation of cell adhesion;multicellular organism development;protein ubiquitination;positive regulation of cell migration;entry of bacterium into host cell;positive regulation of endocytosis;mRNA methylation;cell-cell adhesion
• Cellular component: ubiquitin ligase complex;cytoplasm;cytosol;nuclear speck;RNA N6-methyladenosine methyltransferase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding;identical protein binding;metal ion binding;ubiquitin protein ligase activity