CBLL2

gene
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Also known as FLJ25735HAKAILCT138

Summary

CBLL2 (Cbl proto-oncogene like 2, HGNC:26371) is a protein-coding gene on chromosome Xp22.11, encoding E3 ubiquitin-protein ligase CBLL2 (Q8N7E2). E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins.

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.

Source: NCBI Gene 158506 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 69 total — 7 pathogenic
  • MANE Select transcript: NM_152577

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26371
Approved symbolCBLL2
NameCbl proto-oncogene like 2
LocationXp22.11
Locus typegene with protein product
StatusApproved
AliasesFLJ25735, HAKAIL, CT138
Ensembl geneENSG00000175809
Ensembl biotypeprotein_coding
Entrez158506

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000323684

RefSeq mRNA: 1 — MANE Select: NM_152577 NM_152577

CCDS: CCDS14205

Canonical transcript exons

ENST00000323684 — 1 exons

ExonStartEnd
ENSE000012848542227291322274461

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 84.69.

Top tissues by expression

235 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001984.69gold quality
left testisUBERON:000453372.81gold quality
right testisUBERON:000453470.84gold quality
testisUBERON:000047370.38gold quality
upper leg skinUBERON:000426252.71silver quality
skin of hipUBERON:000155452.52silver quality
adult organismUBERON:000702343.96gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
secondary oocyteCL:000065542.57gold quality
germinal epithelium of ovaryUBERON:000130441.99gold quality
inferior vagus X ganglionUBERON:000536341.75gold quality
vastus lateralisUBERON:000137941.41gold quality
quadriceps femorisUBERON:000137741.37gold quality
superficial temporal arteryUBERON:000161441.33gold quality
palpebral conjunctivaUBERON:000181241.10gold quality
mucosa of paranasal sinusUBERON:000503040.98gold quality
amniotic fluidUBERON:000017340.69gold quality
jejunal mucosaUBERON:000039940.59gold quality
biceps brachiiUBERON:000150740.57gold quality
epithelium of nasopharynxUBERON:000195140.45gold quality
myocardiumUBERON:000234940.45gold quality
gingival epitheliumUBERON:000194940.43gold quality
esophagus squamous epitheliumUBERON:000692040.29gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450240.27gold quality
jejunumUBERON:000211540.18gold quality
mammary ductUBERON:000176540.07gold quality
cartilage tissueUBERON:000241840.06gold quality
oviduct epitheliumUBERON:000480440.03gold quality
mucosa of sigmoid colonUBERON:000499339.95gold quality
bronchial epithelial cellCL:000232839.84gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes2.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting CBLL2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-426799.9666.532368
HSA-MIR-144-3P99.9473.982698
HSA-MIR-101-3P99.9475.032230
HSA-MIR-205-3P99.9269.923165
HSA-MIR-44899.7972.372103
HSA-MIR-370-5P99.7866.81706
HSA-MIR-379-3P99.6969.601524
HSA-MIR-411-3P99.6969.631524
HSA-MIR-584-3P99.3567.691082
HSA-MIR-463598.7467.631339
HSA-MIR-1139998.7165.69869
HSA-MIR-427798.3467.171323
HSA-MIR-93-3P98.1566.651309
HSA-MIR-6847-5P97.9366.741808
HSA-MIR-3928-3P97.6166.531096

Literature-anchored findings (GeneRIF, showing 1)

  • A novel RING finger protein, ZNF645, which is expressed specifically in human testis and sperm and has E3 ubiquitin ligase activity. (PMID:20657603)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
danio_reriocbll1ENSDARG00000015222
drosophila_melanogasterHakaiFBGN0032812

Paralogs (1): CBLL1 (ENSG00000105879)

Protein

Protein identifiers

E3 ubiquitin-protein ligase CBLL2Q8N7E2 (reviewed: Q8N7E2)

Alternative names: Cbl proto-oncogene-like protein 2, RING-type E3 ubiquitin transferase ZNF645, Zinc finger protein 645, c-Cbl-like protein 2

All UniProt accessions (1): Q8N7E2

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. May operate on tyrosine-phosphorylated SRC substrates.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm.

Tissue specificity. Exclusively expressed in testis and sperm, including spermatocytes, round and elongated spermatids, and Leydig cells.

Domain organisation. The HYB domain forms a phosphotyrosine-binding pocket upon dimerization, and mediates as well the recognition of its flanking acidic amino acids.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (1): NP_689790* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR013087Znf_C2H2_typeDomain
IPR017907Znf_RING_CSConserved_site
IPR040380HAKAI-like_RING-HCDomain
IPR040383HAKAI/CBLL2Family
IPR041042Znf_HakaiDomain

Pfam: PF18408

UniProt features (12 total): region of interest 3, zinc finger region 2, sequence conflict 2, compositionally biased region 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N7E2-F155.140.18

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1280218Adaptive Immune System
R-HSA-168256Immune System
R-HSA-983169Class I MHC mediated antigen processing & presentation

MSigDB gene sets: 20 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOCC_TRANSFERASE_COMPLEX, GOCC_METHYLTRANSFERASE_COMPLEX, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_ACTIVITY, chrXp22, YAP1_DN, MIR448, MIR584_3P, MIR3928_3P, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_CONJUGATION

GO Biological Process (2): protein ubiquitination (GO:0016567), regulation of cell adhesion (GO:0030155)

GO Molecular Function (5): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), RNA N6-methyladenosine methyltransferase complex (GO:0036396)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Class I MHC mediated antigen processing & presentation1
Immune System1
Adaptive Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein modification by small protein conjugation1
cell adhesion1
regulation of cellular process1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
methyltransferase complex1

Protein interactions and networks

STRING

434 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CBLL2UBE3DQ7Z6J8589
CBLL2SMCO3A2RU48571
CBLL2OR1J4Q8NGS1506
CBLL2TRIM63Q969Q1471
CBLL2SATL1Q86VE3447
CBLL2OR2B11Q5JQS5420
CBLL2OR5I1Q13606419
CBLL2RNF151Q2KHN1417
CBLL2OR10AD1Q8NGE0398
CBLL2MROH6A6NGR9396
CBLL2CBLP22681394
CBLL2VN1R1Q9GZP7394
CBLL2ARIH2O95376394
CBLL2SEC22CQ9BRL7391
CBLL2CBLCQ9ULV8372

IntAct

25 interactions, top by confidence:

ABTypeScore
KRTAP12-2CBLL2psi-mi:“MI:0915”(physical association)0.560
CYSRT1CBLL2psi-mi:“MI:0915”(physical association)0.560
MAPK9CBLL2psi-mi:“MI:0915”(physical association)0.560
CBLL2PIH1D2psi-mi:“MI:0915”(physical association)0.560
CBLL2PRR13psi-mi:“MI:0915”(physical association)0.560
LONRF1CBLL2psi-mi:“MI:0915”(physical association)0.560
CBLL2MDFIpsi-mi:“MI:0915”(physical association)0.560
CBLL2SRSF10psi-mi:“MI:0914”(association)0.350
CBLL2COL1A1psi-mi:“MI:0914”(association)0.350
CBLL2KRTAP12-2psi-mi:“MI:0915”(physical association)0.000
CBLL2MDFIpsi-mi:“MI:0915”(physical association)0.000
CBLL2CYSRT1psi-mi:“MI:0915”(physical association)0.000
MAPK9CBLL2psi-mi:“MI:0915”(physical association)0.000
PRR13CBLL2psi-mi:“MI:0915”(physical association)0.000
LONRF1CBLL2psi-mi:“MI:0915”(physical association)0.000
CBLL2MAPK9psi-mi:“MI:0915”(physical association)0.000
CBLL2PIH1D2psi-mi:“MI:0915”(physical association)0.000

BioGRID (31): KIAA1429 (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), WTAP (Affinity Capture-MS), ZC3H13 (Affinity Capture-MS), SERTAD4 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), KIAA1429 (Affinity Capture-MS), ZC3H13 (Affinity Capture-MS), SERTAD4 (Affinity Capture-MS), WTAP (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), ZNF645 (Two-hybrid), ZNF645 (Two-hybrid), ZNF645 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVQ3, A0A1W2PPK0, A0A1W2PPM1, A2A9I7, A6NCI8, A6QQS3, A7XCE8, E9PI22, E9PXT9, O15016, O91083, P09414, P0DMB1, P17923, P18804, P20879, P35965, P49750, Q0P670, Q12857, Q1RMX6, Q32LN6, Q32MG2, Q3B8N5, Q3T016, Q3V0A6, Q4JK59, Q5BI31, Q5T035, Q5ZKH6, Q642A3, Q6AXV6, Q6IMN6, Q6P1W5, Q6PEX7, Q6X4T0, Q80YD3, Q86UF4, Q8BII1, Q8C5V0

Diamond homologs: M9PBE2, Q4R361, Q4R7I8, Q4V7X9, Q5ZHZ4, Q75N03, Q8N7E2, Q9JIY2, Q9LFC0

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”CBLL2ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

69 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic7
Likely pathogenic0
Uncertain significance49
Likely benign9
Benign3

Top pathogenic / likely-pathogenic (7)

Variant IDHGVSClassification
1013602NC_000023.11:g.22243338_22690207delPathogenic
438562NC_000023.10:g.22256748_22370988del114241Pathogenic
830979NC_000023.11:g.(?22168312)(22274269_?)delPathogenic
831244NC_000023.10:g.(?21990015)(22292386_?)delPathogenic
831597NC_000023.10:g.(?22094506)(22292386_?)delPathogenic
832361NC_000023.11:g.(?22245333)(22274269_?)delPathogenic
989452NC_000023.11:g.22213388_22345581delPathogenic

SpliceAI

110 predictions. Top by Δscore:

VariantEffectΔscore
X:22273042:G:Tdonor_gain0.7800
X:22274091:A:AGacceptor_gain0.6700
X:22274092:G:GGacceptor_gain0.6700
X:22273042:G:GTdonor_gain0.6300
X:22273334:A:AGacceptor_gain0.5400
X:22273335:G:GGacceptor_gain0.5400
X:22274124:A:Tacceptor_gain0.5300
X:22273074:G:GTdonor_gain0.5200
X:22273335:GTATT:Gacceptor_gain0.5000
X:22274087:C:Gacceptor_gain0.4800
X:22274092:GTT:Gacceptor_gain0.4800
X:22274125:G:Tacceptor_gain0.4700
X:22274092:GTTC:Gacceptor_gain0.4300
X:22273075:A:Tdonor_gain0.4100
X:22274221:ACAT:Aacceptor_gain0.4000
X:22274092:GTTCA:Gacceptor_gain0.3800
X:22274123:CAG:Cacceptor_gain0.3700
X:22273979:AAG:Adonor_gain0.3600
X:22273027:A:Gdonor_gain0.3500
X:22273132:TGAA:Tdonor_gain0.3500
X:22274087:CCTCA:Cacceptor_loss0.3500
X:22274089:TCA:Tacceptor_loss0.3500
X:22274090:CA:Cacceptor_loss0.3500
X:22274091:A:ATacceptor_loss0.3500
X:22274092:G:GCacceptor_loss0.3500
X:22273721:CAGAA:Cacceptor_gain0.3400
X:22274086:A:AGacceptor_gain0.3400
X:22274091:A:Tacceptor_gain0.3400
X:22274082:T:Gacceptor_loss0.3200
X:22274053:A:Gdonor_gain0.3100

AlphaMissense

2790 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:22273325:T:CF112L0.983
X:22273327:C:AF112L0.983
X:22273327:C:GF112L0.983
X:22273220:T:CF77L0.978
X:22273222:T:AF77L0.978
X:22273222:T:GF77L0.978
X:22273197:G:CR69P0.966
X:22273160:T:AC57S0.950
X:22273161:G:CC57S0.950
X:22273225:C:GC78W0.950
X:22273216:T:AH75Q0.948
X:22273216:T:GH75Q0.948
X:22273161:G:AC57Y0.946
X:22273380:T:CL130S0.943
X:22273223:T:CC78R0.942
X:22273268:T:CC93R0.942
X:22273160:T:CC57R0.939
X:22273169:T:AC60S0.938
X:22273170:G:CC60S0.938
X:22273162:T:GC57W0.936
X:22273390:T:AH133Q0.935
X:22273390:T:GH133Q0.935
X:22273193:G:TG68W0.932
X:22273194:G:AG68E0.932
X:22273331:T:AC114S0.932
X:22273332:G:CC114S0.932
X:22273224:G:AC78Y0.931
X:22273131:G:AG47D0.930
X:22273349:T:AC120S0.926
X:22273350:G:CC120S0.926

dbSNP variants (sampled 300 via entrez): RS1002283667 (X:22274957 C>A,T), RS1002708067 (X:22274530 A>T), RS1003159529 (X:22271485 G>A), RS1003619187 (X:22272203 C>T), RS1003703661 (X:22273356 G>A), RS1004248337 (X:22274313 A>G), RS1004681876 (X:22272567 G>C), RS1004819264 (X:22272249 T>C), RS1005250298 (X:22272334 T>C,G), RS1006034157 (X:22274494 G>C), RS1007141629 (X:22271951 T>C,G), RS1007331892 (X:22272250 T>C), RS1008319218 (X:22274914 C>G,T), RS1008613794 (X:22272722 C>G,T), RS1010625281 (X:22273733 G>C,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:307800

GenCC curated gene-disease

Mondo (1): X-linked dominant hypophosphatemic rickets (MONDO:0010619)

Orphanet (1): X-linked hypophosphatemia (Orphanet:89936)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

ChemicalActions (top 5)PubMed papers
CGP 52608affects binding, increases reaction1
Benzo(a)pyreneaffects methylation1
Permethrinincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_XW72HEK293 eGFP-ZNF645Transformed cell lineFemale

Clinical trials (associated diseases)

45 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT03820518PHASE4UNKNOWNUsing Different Doses of Active Vitamin D Combined With Neutral Phosphate in Children With X-linked Hypophosphatemia
NCT04146935PHASE4COMPLETEDExamining the Effect of Burosumab on Muscle Function
NCT04419363PHASE4UNKNOWNBurosumab in Children and Adolescents With X-linked Hypophosphatemia
NCT04842019PHASE4COMPLETEDStudy to Assess the Safety, Pharmacokinetics and Efficacy of KRN23 in Adult Chinese Patients With XLH
NCT04842032PHASE4COMPLETEDStudy to Assess the Safety, Pharmacokinetics and Efficacy of KRN23 in Pediatric Chinese Patients With XLH
NCT02526160PHASE3COMPLETEDStudy of KRN23 in Adults With X-linked Hypophosphatemia (XLH)
NCT02537431PHASE3COMPLETEDOpen Label Study of KRN23 on Osteomalacia in Adults With X-linked Hypophosphatemia (XLH)
NCT02915705PHASE3COMPLETEDEfficacy and Safety of Burosumab Versus Oral Phosphate and Active Vitamin D Treatment in Pediatric Patients With XLH
NCT03233126PHASE3COMPLETEDA Study of KRN23 in Pediatric Patients With X-linked Hypophosphatemic Rickets/Osteomalacia
NCT03920072PHASE3COMPLETEDStudy of the Anti-FGF23 Antibody, Burosumab, in Adults With XLH
NCT04308096PHASE3COMPLETEDA Study of KRN23 in Adult and Pediatric Patients With X-linked Hypophosphatemic Rickets/Osteomalacia
NCT04695860PHASE3COMPLETEDAnti-FGF23 (Burosumab) in Adult Patients With XLH
NCT04872907PHASE3UNKNOWNPrevention of Spontaneous Dental Abscesses in Children With X-linked Hypophosphatemia : a RCT
NCT02163577PHASE2COMPLETEDStudy of KRN23 (Burosumab), a Recombinant Fully Human Monoclonal Antibody Against Fibroblast Growth Factor 23 (FGF23), in Pediatric Subjects With X-linked Hypophosphatemia (XLH)
NCT02312687PHASE2COMPLETEDLong-Term Extension Study of KRN23 in Adult Subjects With X-Linked Hypophosphatemia (XLH)
NCT02750618PHASE2COMPLETEDStudy of the Safety, Pharmacodynamics (PD) and Efficacy of KRN23 in Children From 1 to 4 Years Old With X-linked Hypophosphatemia (XLH)
NCT00195936PHASE1COMPLETEDEffect of Cinacalcet on Parathyroid Hormone Secretion in Children and Adolescents With Hypophosphatemic Rickets
NCT00830674PHASE1COMPLETEDA Study of KRN23 in X-linked Hypophosphatemia
NCT02181764PHASE1COMPLETEDA Study of KRN23 in Subjects With X-linked Hypophosphatemic Rickets/Osteomalacia
NCT01340482PHASE1/PHASE2COMPLETEDA Repeated Study of KRN23 in Adults With X-Linked Hypophosphatemia
NCT01571596PHASE1/PHASE2COMPLETEDAn Extension Study of KRN23 in Adults With X-Linked Hypophosphatemia
NCT02720770PHASE1/PHASE2COMPLETEDGrowth Hormone Treatment in Children With Hypophosphatemic Rickets
NCT04188964PHASE1/PHASE2COMPLETEDStudy to Assess the Safety, Tolerability, Pharmacokinetics and Efficacy of Burosumab in Patients Less Than 1 Year of Age
NCT06525636PHASE1/PHASE2RECRUITINGA First-in-human Study of KK8123 in Adults With X-linked Hypophosphatemia
NCT03748966EARLY_PHASE1COMPLETEDCalcitriol Monotherapy for X-Linked Hypophosphatemia
NCT03771105EARLY_PHASE1RECRUITINGThe Impact of Phosphate Metabolism on Healthy Aging
NCT01652573Not specifiedCOMPLETEDCalcitonin for Treating X-linked Hypophosphatemia
NCT03193476Not specifiedRECRUITINGRegistry for Patients With X-Linked Hypophosphatemia
NCT03489993Not specifiedCOMPLETEDFGF23 and Angiotensin-(1-7) in Hypophosphatemia (GAP)
NCT03596554Not specifiedCOMPLETEDX-linked Hypophosphatemia and FGF21
NCT03651505Not specifiedACTIVE_NOT_RECRUITINGX-linked Hypophosphatemia Disease Monitoring Program
NCT03745521Not specifiedACTIVE_NOT_RECRUITINGStudy of Longitudinal Observation for Patient With X-linked Hypophosphatemic Rickets/Osteomalacia in Collaboration With Asian Partners
NCT03775187Not specifiedAVAILABLEExpanded Access to Burosumab
NCT03879915Not specifiedUNKNOWNDental Implants in Patients With X-linked Hypophosphatemia
NCT04049877Not specifiedCOMPLETEDRetrospective and Prospective Disease Progression and Quality of Life in XLH
NCT04273490Not specifiedCOMPLETEDCharacterising Pain, QoL, Body Composition, Arterial Stiffness, Muscles and Bones in Adult Persons With XLH and Healthy Controls
NCT04946409Not specifiedACTIVE_NOT_RECRUITINGBurden of Disease and Functional Impairment in XLH
NCT05181839Not specifiedCOMPLETEDA Study to Describe the Lived Experience of XLH for Adolescents at End of Skeletal Growth
NCT05312086Not specifiedUNKNOWNMuscle Abnormalities in Children With XLH
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening