IGLL1

gene
On this page

Also known as IGVPBIGL514.1CD179B

Summary

IGLL1 (immunoglobulin lambda like polypeptide 1, HGNC:5870) is a protein-coding gene on chromosome 22q11.23, encoding Immunoglobulin lambda-like polypeptide 1 (P15814). Critical for B-cell development.

The preB cell receptor is found on the surface of proB and preB cells, where it is involved in transduction of signals for cellular proliferation, differentiation from the proB cell to the preB cell stage, allelic exclusion at the Ig heavy chain gene locus, and promotion of Ig light chain gene rearrangements. The preB cell receptor is composed of a membrane-bound Ig mu heavy chain in association with a heterodimeric surrogate light chain. This gene encodes one of the surrogate light chain subunits and is a member of the immunoglobulin gene superfamily. This gene does not undergo rearrangement. Mutations in this gene can result in B cell deficiency and agammaglobulinemia, an autosomal recessive disease in which few or no gamma globulins or antibodies are made. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 3543 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): agammaglobulinemia 2, autosomal recessive (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 5
  • Clinical variants (ClinVar): 271 total
  • Phenotypes (HPO): 38
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_020070

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5870
Approved symbolIGLL1
Nameimmunoglobulin lambda like polypeptide 1
Location22q11.23
Locus typegene with protein product
StatusApproved
AliasesIGVPB, IGL5, 14.1, CD179B
Ensembl geneENSG00000128322
Ensembl biotypeprotein_coding
OMIM146770
Entrez3543

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000249053, ENST00000330377, ENST00000438703

RefSeq mRNA: 3 — MANE Select: NM_020070 NM_001369906, NM_020070, NM_152855

CCDS: CCDS13809, CCDS13810

Canonical transcript exons

ENST00000330377 — 3 exons

ExonStartEnd
ENSE000008794612357496723575082
ENSE000013130832357998523580290
ENSE000035866262357312523573585

Expression profiles

Bgee: expression breadth ubiquitous, 112 present calls, max score 91.67.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 13.5294 / max 4710.0035, expressed in 67 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1933167.629754
1933153.738445
1933171.151834
1933140.626523
1933130.154410
1933180.145920
2094180.082715

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bone marrowUBERON:000237191.67gold quality
bone marrow cellCL:000209287.94gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.88gold quality
left testisUBERON:000453384.90gold quality
right testisUBERON:000453483.75gold quality
testisUBERON:000047381.77gold quality
trabecular bone tissueUBERON:000248381.64gold quality
tendon of biceps brachiiUBERON:000818872.79gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450270.81gold quality
thymusUBERON:000237068.82silver quality
buccal mucosa cellCL:000233666.16gold quality
gluteal muscleUBERON:000200065.61gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451164.92gold quality
vena cavaUBERON:000408763.63gold quality
male germ cellCL:000001563.52gold quality
triceps brachiiUBERON:000150962.91gold quality
spermCL:000001962.57gold quality
monocyteCL:000057662.53gold quality
mononuclear cellCL:000084262.41gold quality
biceps brachiiUBERON:000150762.41gold quality
leukocyteCL:000073862.12gold quality
adult organismUBERON:000702361.24gold quality
tongue squamous epitheliumUBERON:000691960.69gold quality
endothelial cellCL:000011560.11gold quality
jejunal mucosaUBERON:000039957.83gold quality
oral cavityUBERON:000016757.70gold quality
lymph nodeUBERON:000002957.49gold quality
myocardiumUBERON:000234957.28gold quality
gingivaUBERON:000182855.78gold quality
quadriceps femorisUBERON:000137755.60gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 15.

ExperimentMarker?Max mean expression
E-HCAD-4yes3905.92
E-CURD-112yes3411.65
E-MTAB-7407yes3193.07
E-MTAB-9067yes3102.31
E-MTAB-10432yes2497.42
E-CURD-79yes1811.15
E-MTAB-8884yes1472.08
E-GEOD-100618yes1214.98
E-ANND-5yes704.07
E-GEOD-76312yes686.83
E-HCAD-6yes72.25
E-HCAD-10yes15.27
E-MTAB-10042yes11.67
E-CURD-122yes7.18
E-ANND-3yes7.06

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EBF1, IKZF1, IKZF3, MYB, PAX5, PREB, RUNX1, SOX4, SSRP1, TCF3

miRNA regulators (miRDB)

10 targeting IGLL1, 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-449299.8768.253611
HSA-MIR-76299.5866.611994
HSA-MIR-444199.4966.563216
HSA-MIR-449899.4767.422360
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-427099.0266.261987
HSA-MIR-6754-5P98.6065.541627
HSA-MIR-56396.2666.13450
HSA-MIR-380-5P95.6867.32512
HSA-MIR-503-3P92.8966.09537

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 3)

  • Hhydrophobic residues from the lambda5-UR is crucial for the interaction with GAL1 and for pre-BCR clustering. (PMID:23124203)
  • in autosomal recessive agammaglobulinemia a homozygous missense mutation at codon 142 (CCG>with CTG) resulting in a Pro>Leu substitution was identified in exon 3 of the IGLL1 gene; 2 additional silent homozygous substitutions were identified at codons 131 (T>C) and 140 (T>C); sequencing also revealed 2 homozygous single-nucleotide polymorphisms in the noncoding region of exon 3 (PMID:27576013)
  • Irrespective of subtype, Acute Lymphoblastic Leukemia with high levels of IGHM, IGLL1 and VPREB1 are arrested at the pre-B stage and correlate with good prognosis in high-risk pediatric B-cell precursor acute lymphoblastic leukemia. (PMID:27611867)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
mus_musculusIglc2ENSMUSG00000076937
mus_musculusIglc3ENSMUSG00000105547
mus_musculusIglc1ENSMUSG00000105906
mus_musculusIglc4ENSMUSG00000106039
rattus_norvegicusIglc1ENSRNOG00000058590
rattus_norvegicusENSRNOG00000077205
rattus_norvegicusENSRNOG00000079313
rattus_norvegicusENSRNOG00000086508

Paralogs (82): IGHV1OR15-9 (ENSG00000188403), IGKC (ENSG00000211592), IGLC1 (ENSG00000211675), IGLC2 (ENSG00000211677), IGLC3 (ENSG00000211679), IGLC7 (ENSG00000211685), TRDC (ENSG00000211829), IGHA2 (ENSG00000211890), IGHE (ENSG00000211891), IGHG4 (ENSG00000211892), IGHG2 (ENSG00000211893), IGHA1 (ENSG00000211895), IGHG1 (ENSG00000211896), IGHG3 (ENSG00000211897), IGHD (ENSG00000211898), IGHM (ENSG00000211899), IGHV6-1 (ENSG00000211933), IGHV1-2 (ENSG00000211934), IGHV1-3 (ENSG00000211935), IGHV2-5 (ENSG00000211937), IGHV3-7 (ENSG00000211938), IGHV3-11 (ENSG00000211941), IGHV3-13 (ENSG00000211942), IGHV3-15 (ENSG00000211943), IGHV3-16 (ENSG00000211944), IGHV1-18 (ENSG00000211945), IGHV3-20 (ENSG00000211946), IGHV3-21 (ENSG00000211947), IGHV3-23 (ENSG00000211949), IGHV1-24 (ENSG00000211950), IGHV2-26 (ENSG00000211951), IGHV4-28 (ENSG00000211952), IGHV3-33 (ENSG00000211955), IGHV4-34 (ENSG00000211956), IGHV3-35 (ENSG00000211957), IGHV3-38 (ENSG00000211958), IGHV4-39 (ENSG00000211959), IGHV1-45 (ENSG00000211961), IGHV1-46 (ENSG00000211962), IGHV3-48 (ENSG00000211964)

Protein

Protein identifiers

Immunoglobulin lambda-like polypeptide 1P15814 (reviewed: P15814)

Alternative names: CD179 antigen-like family member B, Ig lambda-5, Immunoglobulin omega polypeptide, Immunoglobulin-related protein 14.1

All UniProt accessions (2): P15814, C9JEE0

UniProt curated annotations — full annotation on UniProt →

Function. Critical for B-cell development.

Subunit / interactions. Associates non-covalently with VPREB1. Interacts with SYNV1/HRD1 (via N-terminus); this interaction leads to increased IGLL1 ubiquitination and degradation in pre-B cells, possibly through a lysosomal, not proteasomal, pathway.

Subcellular location. Endoplasmic reticulum. Secreted.

Tissue specificity. Expressed only in pre-B-cells and a special B-cell line (which is surface Ig negative).

Disease relevance. Agammaglobulinemia 2, autosomal recessive (AGM2) [MIM:613500] A primary immunodeficiency characterized by profoundly low or absent serum antibodies and low or absent circulating B cells due to an early block of B-cell development. Affected individuals develop severe infections in the first years of life. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt IDNamesCanonical?
P15814-11yes
P15814-22

RefSeq proteins (3): NP_001356835, NP_064455, NP_690594 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003006Ig/MHC_CSConserved_site
IPR003597Ig_C1-setDomain
IPR007110Ig-like_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050160MHC/ImmunoglobulinFamily

Pfam: PF07654

UniProt features (24 total): strand 8, helix 4, turn 2, region of interest 2, disulfide bond 2, sequence variant 2, signal peptide 1, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
2H3NX-RAY DIFFRACTION2.3
2H32X-RAY DIFFRACTION2.7
2LKQSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P15814-F175.190.53

Antibody-complex structures (SAbDab): 22H32, 2H3N

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (2): 135–194, 212

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-202733Cell surface interactions at the vascular wall

MSigDB gene sets: 213 (showing top): MODULE_478, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_B_CELL_MEDIATED_IMMUNITY, MODULE_75, GOBP_LYMPHOCYTE_MEDIATED_IMMUNITY, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, GOBP_ADAPTIVE_IMMUNE_RESPONSE, GOBP_IMMUNE_EFFECTOR_PROCESS, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, MCCABE_HOXC6_TARGETS_CANCER_UP, MODULE_46, REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL, GOBP_ADAPTIVE_IMMUNE_RESPONSE_BASED_ON_SOMATIC_RECOMBINATION_OF_IMMUNE_RECEPTORS_BUILT_FROM_IMMUNOGLOBULIN_SUPERFAMILY_DOMAINS, WILCOX_RESPONSE_TO_PROGESTERONE_DN, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP

GO Biological Process (2): immune response (GO:0006955), immunoglobulin mediated immune response (GO:0016064)

GO Molecular Function (2): antigen binding (GO:0003823), protein binding (GO:0005515)

GO Cellular Component (4): extracellular region (GO:0005576), endoplasmic reticulum (GO:0005783), membrane (GO:0016020), IgG immunoglobulin complex (GO:0071735)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Hemostasis1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular anatomical structure2
immune system process1
response to stimulus1
B cell mediated immunity1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
immunoglobulin complex1

Protein interactions and networks

STRING

1318 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IGLL1VPREB1P12018999
IGLL1CD79AP11912992
IGLL1CD79BP40259991
IGLL1IGHV4-38-2P0DP08935
IGLL1VPREB3Q9UKI3890
IGLL1PGM3O95394879
IGLL1BLNKQ8WV28815
IGLL1RAG1P15918749
IGLL1RAG2P55895737
IGLL1LRRC8AQ8IWT6733
IGLL1BTKQ06187724
IGLL1CD19P15391698
IGLL1EBF1Q9UH73651
IGLL1JCHAINP01591647
IGLL1DNTTP04053642

IntAct

18 interactions, top by confidence:

ABTypeScore
CD9ADAM10psi-mi:“MI:0914”(association)0.750
IGLL1FAM25Cpsi-mi:“MI:0915”(physical association)0.560
IGLL1UBQLN2psi-mi:“MI:0915”(physical association)0.560
FAM25CIGLL1psi-mi:“MI:0915”(physical association)0.560
IGLL5IGLC7psi-mi:“MI:0914”(association)0.530
IGLL1psi-mi:“MI:0915”(physical association)0.510
IGLL1psi-mi:“MI:0915”(physical association)0.510
IGLL1psi-mi:“MI:0915”(physical association)0.370
IGLL1psi-mi:“MI:0915”(physical association)0.370
IGHG1PDPK1psi-mi:“MI:0914”(association)0.350
IGLL5POTEFpsi-mi:“MI:0914”(association)0.350
GPC3PXDNLpsi-mi:“MI:0914”(association)0.350
MMEHLA-Apsi-mi:“MI:0914”(association)0.350
IGLL1UBQLN2psi-mi:“MI:0915”(physical association)0.000

BioGRID (13): IGLL1 (Affinity Capture-MS), IGLL1 (Two-hybrid), IGLL1 (Affinity Capture-MS), IGLL1 (Affinity Capture-MS), UBQLN2 (Two-hybrid), FAM25A (Two-hybrid), FAM25G (Two-hybrid), FAM25C (Two-hybrid), IGLL1 (Affinity Capture-MS), IGLL1 (Affinity Capture-MS), IGLL1 (Co-fractionation), IGLL1 (Affinity Capture-RNA), IGLL1 (Two-hybrid)

ESM2 similar proteins: A4D1S0, A4K2S4, A6NMD0, B9A064, F8WCM5, H7C350, O00220, O14931, O15533, O70146, O73895, O75298, O76081, P01854, P01883, P14138, P15692, P15814, P16382, P20764, P24394, P49763, P61484, P83743, Q00731, Q0VCS0, Q15569, Q3UM83, Q5R8H1, Q5RFR2, Q5TJE4, Q63257, Q63572, Q68D85, Q6P050, Q6PZD2, Q6WG24, Q7TQM3, Q863Z5, Q8MJ02

Diamond homologs: A0A0A0MT76, B9A064, P15814, A0A5B9, A0M8Q6, P01834, P01835, P01836, P01837, P01838, P01839, P01840, P01841, P01843, P01844, P01845, P01846, P01847, P01850, P01851, P01852, P01854, P01855, P01857, P01859, P01860, P01861, P01862, P01863, P01865, P01867, P01868, P01869, P01871, P01872, P01874, P01921, P03984, P03987, P03988

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance153
Likely benign76
Benign21

Top pathogenic / likely-pathogenic (0)

SpliceAI

254 predictions. Top by Δscore:

VariantEffectΔscore
22:23574965:A:ACdonor_gain1.0000
22:23574966:C:CCdonor_gain1.0000
22:23573582:TGAC:Tacceptor_gain0.9900
22:23573585:CCT:Cacceptor_loss0.9900
22:23573586:C:CAacceptor_loss0.9900
22:23573587:T:Aacceptor_loss0.9900
22:23579979:CCTTA:Cdonor_loss0.9900
22:23579980:CTTA:Cdonor_loss0.9900
22:23579981:TTACC:Tdonor_loss0.9900
22:23579982:TACCT:Tdonor_loss0.9900
22:23579983:A:Cdonor_loss0.9900
22:23579984:C:Tdonor_loss0.9900
22:23573581:CTGAC:Cacceptor_gain0.9800
22:23573586:C:CCacceptor_gain0.9800
22:23573588:G:Cacceptor_gain0.9800
22:23573588:G:GCacceptor_gain0.9800
22:23573595:C:CTacceptor_gain0.9800
22:23579987:G:Adonor_gain0.9800
22:23573583:GAC:Gacceptor_gain0.9700
22:23573590:G:Cacceptor_gain0.9700
22:23573596:A:Tacceptor_gain0.9700
22:23574959:CCACT:Cdonor_loss0.9700
22:23574960:CACTT:Cdonor_loss0.9700
22:23574961:ACTT:Adonor_loss0.9700
22:23574962:CTTAC:Cdonor_loss0.9700
22:23574963:TTA:Tdonor_loss0.9700
22:23574964:TACT:Tdonor_loss0.9700
22:23574965:ACTT:Adonor_loss0.9700
22:23573583:GACC:Gacceptor_gain0.9600
22:23573584:AC:Aacceptor_gain0.9600

AlphaMissense

1362 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:23573461:C:AW149C0.982
22:23573461:C:GW149C0.982
22:23573488:A:CF140L0.981
22:23573488:A:TF140L0.981
22:23573490:A:GF140L0.981
22:23573350:C:AW186C0.967
22:23573350:C:GW186C0.967
22:23573463:A:GW149R0.967
22:23573463:A:TW149R0.967
22:23573504:C:GC135S0.960
22:23573505:A:TC135S0.960
22:23573377:G:CS177R0.949
22:23573377:G:TS177R0.949
22:23573379:T:GS177R0.949
22:23573505:A:GC135R0.949
22:23573327:C:GC194S0.944
22:23573328:A:TC194S0.944
22:23574995:A:CF98L0.939
22:23574995:A:TF98L0.939
22:23574997:A:GF98L0.939
22:23573380:G:CS176R0.931
22:23573380:G:TS176R0.931
22:23573382:T:GS176R0.931
22:23573352:A:GW186R0.928
22:23573352:A:TW186R0.928
22:23573551:G:CF119L0.927
22:23573551:G:TF119L0.927
22:23573553:A:GF119L0.927
22:23573327:C:TC194Y0.909
22:23573328:A:GC194R0.909

dbSNP variants (sampled 300 via entrez): RS1000046947 (22:23576192 C>T), RS1000453116 (22:23582139 C>G,T), RS1000508939 (22:23581194 C>A), RS1001402001 (22:23580787 A>G), RS1001454428 (22:23581050 A>G), RS1001566096 (22:23580392 C>A), RS1001604188 (22:23577753 C>T), RS1002400303 (22:23579718 G>A), RS1002776535 (22:23575165 G>T), RS1003327368 (22:23579061 C>T), RS1004808166 (22:23574788 T>TG), RS1004956328 (22:23579925 C>A), RS1004968479 (22:23579899 A>C,G), RS1005417044 (22:23580118 G>A,T), RS1005472970 (22:23577125 G>C,T)

Disease associations

OMIM: gene MIM:146770 | disease phenotypes: MIM:613500

GenCC curated gene-disease

DiseaseClassificationInheritance
agammaglobulinemia 2, autosomal recessiveStrongAutosomal recessive
autosomal agammaglobulinemiaSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
agammaglobulinemia 2, autosomal recessiveModerateAR

Mondo (2): agammaglobulinemia 2, autosomal recessive (MONDO:0013287), autosomal agammaglobulinemia (MONDO:0011096)

Orphanet (0):

HPO phenotypes

38 total (30 of 38 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000218High palate
HP:0000246Sinusitis
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000377Abnormal pinna morphology
HP:0000389Chronic otitis media
HP:0000403Recurrent otitis media
HP:0000509Conjunctivitis
HP:0000988Skin rash
HP:0001287Meningitis
HP:0001369Arthritis
HP:0001508Failure to thrive
HP:0001581Recurrent skin infections
HP:0001875Decreased total neutrophil count
HP:0001944Dehydration
HP:0001945Fever
HP:0002014Diarrhea
HP:0002024Malabsorption
HP:0002110Bronchiectasis
HP:0002205Recurrent respiratory infections
HP:0002718Recurrent bacterial infections
HP:0002719Recurrent infections
HP:0002720Decreased circulating IgA concentration
HP:0002721Immunodeficiency
HP:0002754Osteomyelitis
HP:0002843Abnormal T cell morphology
HP:0002850Decreased circulating total IgM
HP:0003593Infantile onset
HP:0004432Agammaglobulinemia

GWAS associations

5 associations (top):

StudyTraitp-value
GCST000175_34Height6.000000e-06
GCST001019_2Migraine8.000000e-06
GCST002504_3Peripheral artery disease6.000000e-06
GCST006585_916Blood protein levels4.000000e-25
GCST010724_28HOMA-B (corrected for HOMA-IR)3.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004469HOMA-B

MeSH disease descriptors (1)

DescriptorNameTree numbers
C538056Agammaglobulinemia, non-Bruton type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, affects methylation2
Valproic Acidincreases expression, increases methylation, affects cotreatment2
Zincaffects expression, affects cotreatment, increases expression2
sulforaphanedecreases expression1
butyraldehydedecreases expression1
perfluorooctanoic aciddecreases expression1
aflatoxin B2increases methylation1
Bortezomibdecreases expression1
Air Pollutantsincreases abundance, increases expression1
Air Pollutants, Occupationalaffects expression1
Cisplatindecreases expression1
Curcumindecreases expression1
Diethylhexyl Phthalatedecreases expression1
Hydralazineaffects cotreatment, increases expression1
Progesteronedecreases expression1
Tetradecanoylphorbol Acetateaffects cotreatment, affects expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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