CBLL2

protein-coding

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

Gene summary

This gene encodes a member of the zinc finger domain-containing protein family. This family member contains both a RING-type and a C2H2-type of zinc finger domain, and it may function as an E3 ubiquitin-protein ligase. Protein localization suggests a role in human sperm production and quality control. [provided by RefSeq, Aug 2011]

Previous symbols:

ZNF645

MANE transcript

NM_152577.4

Inheritance

—

ClinVar variants

U:38B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:22,272,913-22,274,461

External References & Databases

Ensembl (ENSG00000175809)

Transcript & Mutation Effects

hg38 • Region Span ~1.5 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 CBLL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152577.4. 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					2 clinvar	2
missense			38 clinvar	10 clinvar	2 clinvar	50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	10	4	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152577.4	RefSeq	NP_689790.1	1	MANE Select
ENST00000323684.4	Ensembl	ENSP00000323348.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Adaptive Immune System
Antigen processing: Ubiquitination & Proteasome degradation
Class I MHC mediated antigen processing & presentation

Biological Process

protein ubiquitination

Molecular Function

nucleic acid binding
metal ion binding
ubiquitin protein ligase activity

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323684
Coding exons: 1
Length: 1510

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: 1.15
RVIS percentile EVS: 92.52

Essentials

Essential (gene trap): N