CBLB

protein-coding

Cbl proto-oncogene B, the group of Ring finger proteins

Gene summary

This gene encodes an E3 ubiquitin-protein ligase which promotes proteosome-mediated protein degradation by transferring ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate. The encoded protein is involved in the regulation of immune response by limiting T-cell receptor, B-cell receptor, and high affinity immunoglobulin epsilon receptor activation. Studies in mouse suggest that this gene is involved in antifungal host defense and that its inhibition leads to increased fungal killing. Manipulation of this gene may be beneficial in implementing immunotherapies for a variety of conditions, including cancer, autoimmune diseases, allergies, and infections. [provided by RefSeq, Sep 2017]

MANE transcript

NM_170662.5

Inheritance

AR

ClinVar variants

P:4U:124B:20

Top phenotype

Autoimmune disease, multisystem, infantile-onset, 3

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr3:105,655,461-105,869,552

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~214.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autoimmune disease, multisystem, infantile-onset, 3LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0957388

Submitter: Ambry Genetics

autoimmune disease, multisystem, infantile-onset, 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0957388

Submitter: Labcorp Genetics (formerly Invitae)

autoimmune disease, multisystem, infantile-onset, 3MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0957388

Submitter: ClinGen

*CBLB* was first reported in relation to multisystem autoimmune infantile-onset disease 3 (PMID: 36006710). At least 3 unique variants (2 missense, 1 nonsense) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Experimental evidence includes biochemical function (PMID: 20624942, 21248250, 11526404, 36165179), protein interaction ( PMID: 19190244, 25560411), evidence of functional alteration (PMID 36006710), mouse model (PMID: 36006710, 10646609, 10646608, 12118252, 17618294), , and mouse rescue model (PMID 12118252, 17618294). Variants in this gene have been reported in at least 3 probands in 1 publication (PMID: 36006710). Genetic variants in CBLB have been reported to be associated autosomal recessive human immune dysregulation-first reported in relation to multisystem autoimmune infantile-onset disease 3 (PMID: 36006710). CBLB encodes CBL-B, a RING-type E3 ubiquitin ligase highly expressed in immune cells. It ubiquitinates receptor-proximal signaling proteins downstream of the TCR, BCR, CD28, and FcεRI, thereby raising the threshold for lymphocyte activation, promoting T-cell anergy, and maintaining peripheral tolerance. A key non-proteolytic action is ubiquitination of the PI3K p85 subunit, uncoupling TCR/CD28 signaling; CBL-B is itself stabilized by CTLA-4 engagement and degraded upon CD28 costimulation. It shares substrates partly redundantly with its paralog CBL. In summary, mechanistically, CBL-B is a negative regulator of lymphocyte activation and peripheral tolerance. In the Janssen et al. (PMID: 36006710) report, three unrelated children with early-onset autoimmunity (one also with chronic urticaria) carrying distinct biallelic CBLB variants have been described: p.R496X (abolished protein), p.C464W (preserved protein), and p.H285L (SH2 domain, reduced expression). Patient T cells had excessive proliferation to anti-CD3, and p.H285L effector T cells were resistant to Treg suppression establishing CBL-B deficiency as a cause of human immune dysregulation. A knock-in mouse (Cblb H257L, orthologous to patient p.H285L) reproduced T/B-cell hyperproliferation, Treg-resistant effector T cells, mast-cell hyperactivation after FcεRI cross-linking, and exaggerated IgE-mediated anaphylaxis providing a strong genotype-matched model concordance. Experimental data demonstrates that the E3 ligase catalytic activity is essential for CBL-B's negative regulation of T cells in vivo, and that Cblb−/− effector T cells are intrinsically resistant to Treg suppression. In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged.​

Clinical Genomic Database (CGD)

Autoimmune disease, multisystem, infantile-onset, 3AR

Manifestation: Allergy/Immunology/Infectious

Intervention: Allergy/Immunology/Infectious

Rationale: The condition may manifest with a variety of autoimmune manifestations, and medical management (eg, with IVIG or corticosteroids) has been described in some individuals

Refs: 36006710Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CBLB variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 123
CBLB-related disorderTotal: 15
not providedTotal: 8
Autoimmune disease, multisystem, infantile-onset, 3Total: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_170662.5. 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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
11
clinvar
5
clinvar
23
missense
2
clinvar
110
clinvar
2
clinvar
2
clinvar
116
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
7
clinvar
8
Total31124137148

Highest pathogenic variant AF is 0.0000020537957

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 84 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_170662.5RefSeqNP_733762.218MANE Select
ENST00000394030.8EnsemblENSP00000377598.418MANE Select
NM_001321786.1RefSeqNP_001308715.119Standard
NM_001321788.2RefSeqNP_001308717.118Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • T cell receptor signaling pathway - Homo sapiens (human)
  • Endocytosis - Homo sapiens (human)
  • Ubiquitin mediated proteolysis - Homo sapiens (human)
  • ErbB signaling pathway - Homo sapiens (human)
  • C-type lectin receptor signaling pathway - Homo sapiens (human)

Biological Process

  • NLS-bearing protein import into nucleus
  • signal transduction
  • cell surface receptor signaling pathway
  • negative regulation of epidermal growth factor-activated receptor activity
  • protein ubiquitination

Molecular Function

  • phosphotyrosine residue binding
  • calcium ion binding
  • protein binding
  • zinc ion binding
  • SH3 domain binding

Cellular Component

  • nucleoplasm
  • cytosol
  • plasma membrane
  • membrane raft

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000264122
Coding exons
18
Length
214092
Individuals with no LoFs
125736
Homozygous LoFs
0
Heterozygous LoFs
12
Defined
125748
p
0.0000477
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.294605450.8440.00002986406
Missense (PolyPhen)151222.530.678562608
Synonymous-0.5251991901.050.00001001942
Loss of Function5.59749.40.1420.00000287580

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000800.000070rare
South Asian00.0absent
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. Negatively regulates TCR (T-cell receptor), BCR (B- cell receptor) and FCER1 (high affinity immunoglobulin epsilon receptor) signal transduction pathways. In naive T-cells, inhibits VAV1 activation upon TCR engagement and imposes a requirement for CD28 costimulation for proliferation and IL-2 production. Also acts by promoting PIK3R1/p85 ubiquitination, which impairs its recruitment to the TCR and subsequent activation. In activated T- cells, inhibits PLCG1 activation and calcium mobilization upon restimulation and promotes anergy. In B-cells, acts by ubiquitinating SYK and promoting its proteasomal degradation. Slightly promotes SRC ubiquitination. May be involved in EGFR ubiquitination and internalization. May be functionally coupled with the E2 ubiquitin-protein ligase UB2D3. {ECO:0000269|PubMed:10022120, ECO:0000269|PubMed:10086340, ECO:0000269|PubMed:11087752, ECO:0000269|PubMed:11526404, ECO:0000269|PubMed:14661060, ECO:0000269|PubMed:20525694}.;

Recessive Scores

pRec
0.382

Intolerance Scores

LoFtool
0.104
RVIS EVS
-0.84
RVIS percentile EVS
11.4

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.859

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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