IGSF11

gene
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Also known as BT-IgSFMGC35227Igsf13VSIG3CT119

Summary

IGSF11 (immunoglobulin superfamily member 11, HGNC:16669) is a protein-coding gene on chromosome 3q13.32, encoding Immunoglobulin superfamily member 11 (Q5DX21). Functions as a cell adhesion molecule through homophilic interaction.

IGSF11 is an immunoglobulin (Ig) superfamily member that is preferentially expressed in brain and testis. It shares significant homology with coxsackievirus and adenovirus receptor (CXADR; MIM 602621) and endothelial cell-selective adhesion molecule (ESAM).

Source: NCBI Gene 152404 — RefSeq curated summary.

At a glance

  • GWAS associations: 24
  • Clinical variants (ClinVar): 68 total
  • Druggable target: yes
  • MANE Select transcript: NM_001015887

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16669
Approved symbolIGSF11
Nameimmunoglobulin superfamily member 11
Location3q13.32
Locus typegene with protein product
StatusApproved
AliasesBT-IgSF, MGC35227, Igsf13, VSIG3, CT119
Ensembl geneENSG00000144847
Ensembl biotypeprotein_coding
OMIM608351
Entrez152404

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000354673, ENST00000393775, ENST00000425327, ENST00000441144, ENST00000459718, ENST00000480431, ENST00000483401, ENST00000489689, ENST00000491903, ENST00000494802, ENST00000874675, ENST00000874676, ENST00000874677, ENST00000947895

RefSeq mRNA: 11 — MANE Select: NM_001015887 NM_001015887, NM_001353318, NM_001353319, NM_001353320, NM_001353321, NM_001353322, NM_001353323, NM_001353324, NM_001353325, NM_001353326, NM_152538

CCDS: CCDS2983, CCDS46891, CCDS87123, CCDS87124, CCDS87125

Canonical transcript exons

ENST00000393775 — 7 exons

ExonStartEnd
ENSE00000967477118926101118926256
ENSE00001241518118904648118904798
ENSE00001241526118905596118905718
ENSE00001851354118900557118902961
ENSE00001953097119034531119034846
ENSE00003497813118928509118928716
ENSE00003623791118930112118930275

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 97.36.

FANTOM5 (CAGE): breadth broad, TPM avg 3.2818 / max 192.4690, expressed in 295 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter IDTPM avgSamples expressed
439641.2343195
439631.1153180
439620.2324103
439660.214587
439600.160283
439650.139589
439610.107767
439670.034318
439700.02883
439690.01066

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065597.36gold quality
oocyteCL:000002397.27gold quality
corpus callosumUBERON:000233692.11gold quality
left testisUBERON:000453391.47gold quality
right testisUBERON:000453490.85gold quality
spinal cordUBERON:000224090.00gold quality
C1 segment of cervical spinal cordUBERON:000646989.99gold quality
testisUBERON:000047389.92gold quality
medial globus pallidusUBERON:000247789.52gold quality
inferior vagus X ganglionUBERON:000536389.27gold quality
globus pallidusUBERON:000187588.81gold quality
caudate nucleusUBERON:000187386.60gold quality
ventricular zoneUBERON:000305386.40gold quality
subthalamic nucleusUBERON:000190686.18gold quality
Brodmann (1909) area 46UBERON:000648386.10gold quality
putamenUBERON:000187485.83gold quality
medulla oblongataUBERON:000189685.10gold quality
substantia nigraUBERON:000203885.07gold quality
midbrainUBERON:000189184.66gold quality
nucleus accumbensUBERON:000188284.56gold quality
prefrontal cortexUBERON:000045184.40gold quality
amygdalaUBERON:000187684.16gold quality
Ammon’s hornUBERON:000195484.00gold quality
ponsUBERON:000098883.84gold quality
temporal lobeUBERON:000187183.79gold quality
postcentral gyrusUBERON:000258183.78gold quality
middle temporal gyrusUBERON:000277183.56gold quality
Brodmann (1909) area 9UBERON:001354083.33gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.24gold quality
entorhinal cortexUBERON:000272883.16gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.70
E-CURD-10no8.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

156 targeting IGSF11, 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-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4262100.0073.263931
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-186-5P99.9970.833707
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-607799.9968.042299
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-453499.9966.581907
HSA-MIR-428299.9975.366408
HSA-MIR-1213699.9872.815713
HSA-MIR-569699.9872.364487
HSA-MIR-548N99.9871.944170
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-433-3P99.9869.371203
HSA-MIR-314899.9775.066478
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-548AN99.9770.912817

Literature-anchored findings (GeneRIF, showing 7)

  • Molecular cloning of BT-IgSF which is preferentially expressed by brain and testis (PMID:12207903)
  • cell adhesion-inducing function of BT-IgSF suggests a role of the cell surface molecule in the development/function of the central nervous system and spermatogenesis (PMID:15795899)
  • IGSF11 is a good candidate of cancer-testis antigen. Furthermore, suppression of IGSF11 by siRNA retarded the growth of gastric cancer cells. (PMID:16108831)
  • Concerted role for IgSF11 and PSD-95 in the regulation of AMPAR-mediated synaptic transmission and plasticity. (PMID:26595655)
  • this study shows that VSIG-3 as a ligand of VISTA inhibits human T-cell function (PMID:30220083)
  • Structural Basis of VSIG3: The Ligand for VISTA. (PMID:33841409)
  • IGSF11 is required for pericentric heterochromatin dissociation during meiotic diplotene. (PMID:34491997)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioigsf11ENSDARG00000109783
mus_musculusIgsf11ENSMUSG00000022790
rattus_norvegicusIgsf11ENSRNOG00000001525

Paralogs (14): VSIG2 (ENSG00000019102), VSIG1 (ENSG00000101842), VSIR (ENSG00000107738), GPA33 (ENSG00000143167), ESAM (ENSG00000149564), CXADR (ENSG00000154639), JAM2 (ENSG00000154721), F11R (ENSG00000158769), MXRA8 (ENSG00000162576), JAM3 (ENSG00000166086), CLMP (ENSG00000166250), MUC15 (ENSG00000169550), VSTM2B (ENSG00000187135), VSIG8 (ENSG00000243284)

Protein

Protein identifiers

Immunoglobulin superfamily member 11Q5DX21 (reviewed: Q5DX21)

Alternative names: Brain and testis-specific immunoglobulin superfamily protein, V-set and immunoglobulin domain-containing protein 3

All UniProt accessions (5): Q5DX21, C9IZX3, C9JAD3, C9JBA5, C9JMW0

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a cell adhesion molecule through homophilic interaction. Stimulates cell growth.

Subcellular location. Cell membrane.

Tissue specificity. Abundantly expressed in testis and ovary and to a lower extent in brain, kidney and skeletal muscle.

Post-translational modifications. N-glycosylated.

Miscellaneous. The last 20 cytoplasmic amino acids are not required for the cell adhesion function.

Isoforms (3)

UniProt IDNamesCanonical?
Q5DX21-11yes
Q5DX21-22
Q5DX21-33

RefSeq proteins (11): NP_001015887, NP_001340247, NP_001340248, NP_001340249, NP_001340250, NP_001340251, NP_001340252, NP_001340253, NP_001340254, NP_001340255, NP_689751 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR042758IGSF11Family

Pfam: PF07686, PF13927

UniProt features (21 total): sequence variant 3, sequence conflict 3, disulfide bond 2, splice variant 2, topological domain 2, domain 2, signal peptide 1, chain 1, glycosylation site 1, transmembrane region 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5DX21-F173.380.47

Functional residue map

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

Post-translational modifications (1): 378

Disulfide bonds (2): 44–120, 165–215

Glycosylation sites (1): 102

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GOBP_SYNAPSE_ASSEMBLY, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_REGULATION_OF_SYNAPTIC_PLASTICITY, GOBP_REGULATION_OF_SYNAPSE_ASSEMBLY, ATTCTTT_MIR186, GOBP_SYNAPTIC_SIGNALING, GOBP_POSITIVE_REGULATION_OF_LONG_TERM_SYNAPTIC_POTENTIATION, GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY, GOBP_LONG_TERM_SYNAPTIC_POTENTIATION, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_LONG_TERM_SYNAPTIC_POTENTIATION

GO Biological Process (7): homophilic cell-cell adhesion (GO:0007156), obsolete cell-cell adhesion via plasma-membrane adhesion molecules (GO:0098742), trans-synaptic signaling (GO:0099537), positive regulation of long-term synaptic potentiation (GO:1900273), regulation of presynapse assembly (GO:1905606), cell adhesion (GO:0007155), regulation of synaptic plasticity (GO:0048167)

GO Molecular Function (2): ionotropic glutamate receptor binding (GO:0035255), protein binding (GO:0005515)

GO Cellular Component (4): plasma membrane (GO:0005886), cell-cell junction (GO:0005911), synapse (GO:0045202), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell-cell adhesion1
synaptic signaling1
positive regulation of synaptic transmission1
long-term synaptic potentiation1
regulation of long-term synaptic potentiation1
regulation of synapse assembly1
presynapse assembly1
regulation of presynapse organization1
cellular process1
modulation of chemical synaptic transmission1
regulation of biological quality1
glutamate receptor binding1
binding1
membrane1
cell periphery1
anchoring junction1
cell junction1
cellular anatomical structure1

Protein interactions and networks

STRING

850 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IGSF11VSIRQ9H7M9740
IGSF11CSF1RP07333573
IGSF11HAVCR2Q8TDQ0571
IGSF11LAG3P18627561
IGSF11CTLA4P16410551
IGSF11TIGITQ495A1541
IGSF11BTLAQ7Z6A9484
IGSF11KCNJ13O60928479
IGSF11VSIG1Q86XK7454
IGSF11TNFRSF18Q9Y5U5433
IGSF11PPP1R36Q96LQ0420
IGSF11LRFN2Q9ULH4406
IGSF11DNAJC24Q6P3W2406
IGSF11MAU2Q9Y6X3400
IGSF11MCHR1Q99705399

IntAct

3 interactions, top by confidence:

ABTypeScore
IGSF11IGSF11psi-mi:“MI:0915”(physical association)0.400
IGSF10IGSF11psi-mi:“MI:0915”(physical association)0.400

BioGRID (2): IGSF11 (Two-hybrid), IGSF11 (Reconstituted Complex)

ESM2 similar proteins: A0A0R4IGV4, A0A8M2B818, A0JM41, A2VD98, B0CLX4, B6ZK77, D3YX43, F1LW30, O00241, O18906, O54901, O88775, O95256, P00545, P04218, P0C673, P10522, P13369, P17948, P21995, P27931, P35916, P35917, P35969, P37301, P42071, P42703, P53767, Q08DK1, Q15762, Q58EG3, Q5DX21, Q5FWR8, Q5R412, Q5U2P2, Q5VJ70, Q6GMZ9, Q6PCB8, Q6X936, Q7TSN7

Diamond homologs: P01635, P01636, P01670, P01671, P01674, P01685, P01696, P04945, P09564, P0C673, P50283, Q08DK1, Q5DX21, Q5U2P2, A2AJ76, D3YXG0, P78310, Q08E08, Q29RR6, Q4KLY3, Q5R764, Q6AYD4, Q6WRH9, Q6WRI0, Q86XK7, Q8K1G0, Q8NDA2, Q8R373, Q90W79, Q90Y50, Q91664, Q925F2, Q92626, Q96IQ7, Q96JA1, Q96RW7, Q99795, Q9D2J4, Q9H6B4, Q9JMB8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance55
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3146 predictions. Top by Δscore:

VariantEffectΔscore
3:118902958:CTCT:Cacceptor_gain1.0000
3:118902960:CT:Cacceptor_gain1.0000
3:118902962:C:CCacceptor_gain1.0000
3:118904643:CAAA:Cdonor_gain1.0000
3:118904644:AAACC:Adonor_loss1.0000
3:118904645:AACCT:Adonor_loss1.0000
3:118904646:A:Cdonor_loss1.0000
3:118905594:A:ACdonor_gain1.0000
3:118905595:C:CCdonor_gain1.0000
3:118905719:C:CCacceptor_gain1.0000
3:118926099:AC:Adonor_gain1.0000
3:118926100:CC:Cdonor_gain1.0000
3:118926257:C:CCacceptor_gain1.0000
3:118930108:ATACC:Adonor_loss1.0000
3:118930110:A:ATdonor_loss1.0000
3:118930273:CAC:Cacceptor_gain1.0000
3:118930276:C:CAacceptor_loss1.0000
3:118930276:C:CCacceptor_gain1.0000
3:118931311:A:ACdonor_gain1.0000
3:118931312:A:Cdonor_gain1.0000
3:118932408:C:Adonor_gain1.0000
3:118958427:T:Adonor_gain1.0000
3:118902957:CCTCT:Cacceptor_gain0.9900
3:118902958:CTCTC:Cacceptor_gain0.9900
3:118902959:TCT:Tacceptor_gain0.9900
3:118902959:TCTCT:Tacceptor_gain0.9900
3:118902960:CTC:Cacceptor_gain0.9900
3:118902961:TC:Tacceptor_loss0.9900
3:118902961:TCT:Tacceptor_gain0.9900
3:118902962:C:Gacceptor_gain0.9900

AlphaMissense

2791 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:118905655:C:GC215S1.000
3:118905656:A:TC215S1.000
3:118926147:C:AW178C1.000
3:118926147:C:GW178C1.000
3:118926149:A:GW178R1.000
3:118926149:A:TW178R1.000
3:118928581:A:CY118D1.000
3:118905642:A:CN219K0.999
3:118905642:A:TN219K0.999
3:118905654:G:CC215W0.999
3:118905655:C:TC215Y0.999
3:118905656:A:GC215R0.999
3:118905662:A:CY213D0.999
3:118926148:C:GW178S0.999
3:118926186:A:CC165W0.999
3:118926187:C:GC165S0.999
3:118926187:C:TC165Y0.999
3:118926188:A:GC165R0.999
3:118926188:A:TC165S0.999
3:118926236:A:GC149R0.999
3:118928520:A:GL138P0.999
3:118928574:C:GC120S0.999
3:118928575:A:GC120R0.999
3:118928575:A:TC120S0.999
3:118905621:A:CC226W0.998
3:118905655:C:AC215F0.998
3:118926160:G:CP174R0.998
3:118926166:G:TP172H0.998
3:118926193:A:GL163P0.998
3:118926234:G:CC149W0.998

dbSNP variants (sampled 300 via entrez): RS1000031433 (3:118946585 G>A), RS1000032365 (3:119074138 A>C), RS1000034318 (3:119086273 T>C), RS1000034569 (3:119022563 G>A), RS1000039251 (3:118928814 C>T), RS1000040493 (3:119019729 T>C), RS1000067000 (3:119107052 G>C), RS1000082237 (3:119129092 T>A), RS1000083079 (3:118948933 C>A,T), RS1000083181 (3:119143559 C>A,T), RS1000092295 (3:118929217 T>A,C), RS1000107436 (3:119015947 A>G), RS1000121460 (3:118974785 T>C), RS1000130003 (3:118952952 T>C), RS1000139335 (3:118915520 A>G)

Disease associations

OMIM: gene MIM:608351 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

StudyTraitp-value
GCST001651_37Response to amphetamines9.000000e-06
GCST001762_178Obesity-related traits1.000000e-06
GCST002541_1Menarche (age at onset)2.000000e-27
GCST003059_8Parkinson’s disease1.000000e-06
GCST003123_11Severe influenza A (H1N1) infection2.000000e-10
GCST003559_2Bone mineral density (hip)1.000000e-09
GCST003559_4Bone mineral density (hip)4.000000e-10
GCST004904_138Body mass index3.000000e-09
GCST005987_30Albumin-globulin ratio2.000000e-08
GCST007323_18Risk-taking tendency (4-domain principal component model)9.000000e-09
GCST007323_79Risk-taking tendency (4-domain principal component model)2.000000e-10
GCST007326_67Number of sexual partners8.000000e-09
GCST007327_19Smoking status (ever vs never smokers)2.000000e-08
GCST007327_212Smoking status (ever vs never smokers)4.000000e-16
GCST007327_90Smoking status (ever vs never smokers)7.000000e-10
GCST007327_96Smoking status (ever vs never smokers)1.000000e-09
GCST008358_3Response to cognitive-behavioural therapy in anxiety and major depressive disorders5.000000e-06
GCST008360_5Response to cognitive-behavioural therapy in anxiety disorder6.000000e-06
GCST008595_38Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)4.000000e-08
GCST008810_25Smoking initiation (ever regular vs never regular)8.000000e-09
GCST008810_53Smoking initiation (ever regular vs never regular)9.000000e-10
GCST008839_418Height4.000000e-10
GCST010002_436Refractive error6.000000e-16
GCST011703_63Smoking initiation1.000000e-09

EFO canonical traits (12, from GWAS)

EFO IDTrait name
EFO:0005118IGFBP-1 measurement
EFO:0004703age at menarche
EFO:1001488influenza A (H1N1)
EFO:0007702hip bone mineral density
EFO:0004340body mass index
EFO:0005128albumin:globulin ratio measurement
EFO:0008579risk-taking behaviour
EFO:0004318smoking behavior
EFO:0007820cognitive behavioural therapy
EFO:0004337intelligence
EFO:0004784self reported educational attainment
EFO:0005670smoking initiation

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5291534 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation6
entinostatdecreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Aflatoxin B1decreases methylation, increases methylation2
FR900359increases phosphorylation1
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
trichostatin Aincreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
perfluorooctanoic acidincreases expression1
benzo(e)pyreneincreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
licochalcone Bincreases expression1
Decitabineaffects expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, decreases methylation1
Cisplatinaffects expression1
Estradiolaffects binding, increases expression1
Leadaffects expression1
Lipopolysaccharidesincreases expression, affects response to substance1
Methapyrileneincreases methylation1
Nickeldecreases expression1
Silicon Dioxidedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5233350BindingBinding affinity to recombinant human VSIG3 (23 to 241 residues extracellular binding domain expressed in Escherichia coli BL21 (DE3) incubated for 30 mins by microscale thermophoresis analysisVISTA inhibitors in cancer immunotherapy: a short perspective on recent progresses. — RSC Med Chem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.