CBLL2

Cbl proto-oncogene like 2, the group of Ring finger proteins

Basic information

Region (hg38): X:22272913-22274461

Previous symbols: [ "ZNF645" ]

Links

ENSG00000175809 ∙ NCBI:158506 ∙ ∙ HGNC:26371 ∙ Uniprot:Q8N7E2 ∙ 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 CBLL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLL2 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					2	2
missense			25	3	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	4

Variants in CBLL2

This is a list of pathogenic ClinVar variants found in the CBLL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-22273071-T-A		not specified	Uncertain significance (Sep 02, 2024)
X-22273089-T-A			Benign (Apr 04, 2018)
X-22273272-C-T		not specified	Uncertain significance (Jul 11, 2023)
X-22273275-G-A		not specified	Uncertain significance (Aug 12, 2021)
X-22273313-C-G		not specified	Uncertain significance (Oct 03, 2022)
X-22273334-A-T		not specified	Uncertain significance (May 26, 2024)
X-22273340-G-C		not specified	Uncertain significance (Nov 08, 2022)
X-22273437-C-T		not specified	Uncertain significance (Oct 29, 2024)
X-22273467-C-T		not specified	Uncertain significance (Nov 21, 2024)
X-22273514-G-T		not specified	Uncertain significance (Apr 06, 2023)
X-22273530-T-A			Benign (Dec 31, 2019)
X-22273568-G-C		not specified	Uncertain significance (Apr 25, 2022)
X-22273578-T-C		not specified	Uncertain significance (Nov 08, 2022)
X-22273623-C-T		not specified	Uncertain significance (Mar 20, 2024)
X-22273629-C-A		not specified	Uncertain significance (Aug 10, 2021)
X-22273635-T-G		not specified	Uncertain significance (Jan 10, 2025)
X-22273636-A-C			Benign (Dec 31, 2019)
X-22273719-T-C		not specified	Uncertain significance (Jun 22, 2023)
X-22273722-A-G		not specified	Uncertain significance (Mar 15, 2024)
X-22273800-C-T		not specified	Uncertain significance (Jan 26, 2022)
X-22273819-A-G		not specified	Likely benign (Feb 23, 2023)
X-22273839-C-T		not specified	Uncertain significance (May 26, 2024)
X-22273866-T-G		not specified	Uncertain significance (Oct 19, 2024)
X-22273920-G-A		not specified	Conflicting classifications of pathogenicity (Feb 01, 2023)
X-22273925-C-G		not specified	Uncertain significance (May 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBLL2	protein_coding	protein_coding	ENST00000323684	1	1510

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.310	168	180	0.935	0.0000146	2787
Missense in Polyphen		18	19.718	0.91287		358
Synonymous	0.214	65	67.2	0.967	0.00000568	834
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (PubMed:20657603). May operate on tyrosine-phosphorylated SRC substrates (PubMed:22252131). {ECO:0000269|PubMed:20657603, ECO:0000269|PubMed:22252131}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Intolerance Scores

• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.52

Haploinsufficiency Scores

• pHI: 0.0442
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: cytoplasm
• Molecular function: nucleic acid binding;metal ion binding;ubiquitin protein ligase activity