IGSF9B

gene
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Also known as KIAA1030LINC00947LOC283174

Summary

IGSF9B (immunoglobulin superfamily member 9B, HGNC:32326) is a protein-coding gene on chromosome 11q25, encoding Protein turtle homolog B (Q9UPX0). Transmembrane protein which is abundantly expressed in interneurons, where it may regulate inhibitory synapse development.

Predicted to enable kinase binding activity. Predicted to be involved in synaptic membrane adhesion. Predicted to act upstream of or within homophilic cell adhesion via plasma membrane adhesion molecules and positive regulation of inhibitory postsynaptic potential. Predicted to be located in dendrite; inhibitory synapse; and neuronal cell body. Predicted to be active in GABA-ergic synapse; neuron projection; and postsynaptic specialization of symmetric synapse.

Source: NCBI Gene 22997 — RefSeq curated summary.

At a glance

  • GWAS associations: 20
  • Clinical variants (ClinVar): 37 total — 1 pathogenic
  • MANE Select transcript: NM_001277285

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:32326
Approved symbolIGSF9B
Nameimmunoglobulin superfamily member 9B
Location11q25
Locus typegene with protein product
StatusApproved
AliasesKIAA1030, LINC00947, LOC283174
Ensembl geneENSG00000080854
Ensembl biotypeprotein_coding
OMIM613773
Entrez22997

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000321016, ENST00000526663, ENST00000527648, ENST00000530957, ENST00000533160, ENST00000533871, ENST00000564347

RefSeq mRNA: 1 — MANE Select: NM_001277285 NM_001277285

CCDS: CCDS61010

Canonical transcript exons

ENST00000533871 — 20 exons

ExonStartEnd
ENSE00000749102133924820133924904
ENSE00001195000133937810133937961
ENSE00001303640133919742133921397
ENSE00001305564133922569133922730
ENSE00001330226133922177133922222
ENSE00001464611133944220133944366
ENSE00001464612133946061133946258
ENSE00001559691133956691133956968
ENSE00003696918133929671133929782
ENSE00003696945133936053133936194
ENSE00003698548133935617133935762
ENSE00003698866133911886133912007
ENSE00003700209133932071133932213
ENSE00003700669133931453133931569
ENSE00003700678133930984133931134
ENSE00003701640133926916133927091
ENSE00003702105133931655133931795
ENSE00003702163133937376133937493
ENSE00003702420133925739133925965
ENSE00003755277133896438133909277

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 94.19.

FANTOM5 (CAGE): breadth broad, TPM avg 2.7744 / max 176.7867, expressed in 679 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1232522.1856631
1232470.3229125
1232510.095648
1232410.069123
1232460.047113
1232480.02838
1232490.025913

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489094.19gold quality
cerebellar hemisphereUBERON:000224594.02gold quality
cerebellar cortexUBERON:000212993.97gold quality
cerebellumUBERON:000203793.91gold quality
lower esophagus muscularis layerUBERON:003583391.25gold quality
lower esophagusUBERON:001347391.16gold quality
cardiac muscle of right atriumUBERON:000337990.98gold quality
cerebellar vermisUBERON:000472090.88gold quality
right coronary arteryUBERON:000162589.60gold quality
descending thoracic aortaUBERON:000234589.43gold quality
popliteal arteryUBERON:000225089.20gold quality
esophagogastric junction muscularis propriaUBERON:003584189.19gold quality
tibial arteryUBERON:000761089.16gold quality
aortaUBERON:000094788.67gold quality
mucosa of stomachUBERON:000119988.65gold quality
thoracic aortaUBERON:000151588.17gold quality
ascending aortaUBERON:000149688.01gold quality
left coronary arteryUBERON:000162687.51gold quality
left uterine tubeUBERON:000130387.39gold quality
body of uterusUBERON:000985387.02gold quality
coronary arteryUBERON:000162186.89gold quality
muscle layer of sigmoid colonUBERON:003580586.11gold quality
middle temporal gyrusUBERON:000277185.25gold quality
right uterine tubeUBERON:000130284.92gold quality
heart left ventricleUBERON:000208483.44gold quality
cardiac ventricleUBERON:000208283.11gold quality
cardiac atriumUBERON:000208183.07gold quality
heartUBERON:000094882.93gold quality
apex of heartUBERON:000209882.91gold quality
right atrium auricular regionUBERON:000663182.80gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-35yes827.90
E-ANND-3no2.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting IGSF9B, 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-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4455100.0065.481587
HSA-MIR-607799.9968.042299
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-444799.8567.812900
HSA-MIR-76599.8468.242442
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-494-3P99.7071.452795
HSA-MIR-7-5P99.6770.531809
HSA-MIR-447299.5666.081478
HSA-MIR-312899.5067.851258
HSA-MIR-442699.1766.741949
HSA-MIR-491-5P99.1365.981468
HSA-MIR-128699.0966.231046
HSA-MIR-877-3P99.0968.101637
HSA-MIR-5000-3P98.7965.631251
HSA-MIR-1211498.7063.45730
HSA-MIR-4662B98.3366.371163
HSA-MIR-464798.3066.411139
HSA-MIR-6881-3P98.0468.241777

Literature-anchored findings (GeneRIF, showing 5)

  • The transcriptional level of MIR4697HG in cancerous tissues increased twofold compared with that in adjacent noncancerous tissues. MIR4697HG was differentially expressed in ovarian cancer cell lines, with the highest levels in OVCAR3 and SKOV3 cells. (PMID:28168162)
  • Polymorphism in IGSF9B gene is associated with schizophrenia and bipolar disorder. (PMID:28786528)
  • The Genetic variants located in IGSF9B has the potential to modulate disease course in MS patients and may be used as disease activity biomarkers to identify patients with divergent disease courses. (PMID:30217166)
  • The role of cell adhesion molecule IgSF9b at the inhibitory synapse and psychiatric disease. (PMID:38029609)
  • LncRNA MIR4697HG Alleviates Endothelial Cell Injury and Atherosclerosis Progression in Mice via the FUS/ANXA5 Axis. (PMID:38082058)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioigsf9bbENSDARG00000069467
mus_musculusIgsf9bENSMUSG00000034275
rattus_norvegicusIgsf9bENSRNOG00000009253

Paralogs (36): CNTN1 (ENSG00000018236), CDON (ENSG00000064309), NEO1 (ENSG00000067141), SDK2 (ENSG00000069188), IGSF9 (ENSG00000085552), NRCAM (ENSG00000091129), MXRA5 (ENSG00000101825), IGDCC4 (ENSG00000103742), CNTN3 (ENSG00000113805), IGSF21 (ENSG00000117154), CNTN6 (ENSG00000134115), CHL1 (ENSG00000134121), PTPRQ (ENSG00000139304), CNTN4 (ENSG00000144619), BOC (ENSG00000144857), SDK1 (ENSG00000146555), HMCN2 (ENSG00000148357), NCAM1 (ENSG00000149294), CNTN5 (ENSG00000149972), IGSF10 (ENSG00000152580), ROBO4 (ENSG00000154133), ROBO3 (ENSG00000154134), NCAM2 (ENSG00000154654), VCAM1 (ENSG00000162692), NFASC (ENSG00000163531), PRTG (ENSG00000166450), ROBO1 (ENSG00000169855), DSCAM (ENSG00000171587), IGDCC3 (ENSG00000174498), VSIG10 (ENSG00000176834), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), VSIG10L (ENSG00000186806), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

Protein turtle homolog BQ9UPX0 (reviewed: Q9UPX0)

Alternative names: Immunoglobulin superfamily member 9B

All UniProt accessions (3): Q9UPX0, E9PRP3, H0YDP1

UniProt curated annotations — full annotation on UniProt →

Function. Transmembrane protein which is abundantly expressed in interneurons, where it may regulate inhibitory synapse development. May mediate homophilic cell adhesion. Is involved in the organization and maintenance of axon initial segment (AIS) architecture, likely cooperating with PRICKLE2 to regulate ANK3/ANKG localization to AIS.

Subunit / interactions. Found in a complex with MAGI2 and NLGN2, where it interacts with MAGI2 (via PDZ 5 and PDZ 6 domains). Interacts with PRICKLE2; the interaction is required for correct IGSF9B and ANK3/ANKG localization in axons.

Subcellular location. Postsynaptic cell membrane. Postsynaptic density. Cell projection. Axon.

Post-translational modifications. N-glycosylated and sialylated. Not significantly O-glycosylated.

Similarity. Belongs to the immunoglobulin superfamily. Turtle family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UPX0-11yes
Q9UPX0-22

RefSeq proteins (1): NP_001264214* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR003961FN3_domDomain
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR051170Neural/epithelial_adhesionFamily

Pfam: PF00041, PF13895, PF13927

UniProt features (40 total): domain 7, compositionally biased region 7, modified residue 6, disulfide bond 5, region of interest 3, glycosylation site 3, topological domain 2, sequence variant 2, signal peptide 1, chain 1, transmembrane region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UPX0-F162.710.29

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 (6): 775, 783, 794, 1136, 1207, 1215

Disulfide bonds (5): 45–113, 161–208, 250–303, 346–397, 442–488

Glycosylation sites (3): 241, 258, 624

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 125 (showing top): MORF_RAGE, TGGTGCT_MIR29A_MIR29B_MIR29C, CAR_TNFRSF25, XU_GH1_AUTOCRINE_TARGETS_UP, AREB6_01, MEF2_02, MORF_FANCG, CAR_MYST2, HFH4_01, HFH3_01, CAR_MLANA, TATA_C, MORF_PML, GOCC_NEURON_PROJECTION, MORF_PDPK1

GO Biological Process (2): cell adhesion (GO:0007155), nervous system development (GO:0007399)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): postsynaptic density (GO:0014069), neuron projection (GO:0043005), postsynaptic membrane (GO:0045211), GABA-ergic synapse (GO:0098982), plasma membrane (GO:0005886), membrane (GO:0016020), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular process1
system development1
binding1
asymmetric synapse1
postsynaptic specialization1
plasma membrane bounded cell projection1
synaptic membrane1
postsynapse1
synapse1
membrane1
cell periphery1
cellular anatomical structure1
cell junction1

Protein interactions and networks

STRING

828 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IGSF9BNLGN2Q8NFZ4707
IGSF9BMAGI2Q86UL8565
IGSF9BELFN1P0C7U0528
IGSF9BIGSF21Q96ID5490
IGSF9BLHFPL4Q7Z7J7464
IGSF9BGAD1Q99259439
IGSF9BDLX1P56177428
IGSF9BNRXN2Q9P2S2425
IGSF9BNRXN1Q9ULB1419
IGSF9BKCNC3Q14003404
IGSF9BLHFPL3Q86UP9399
IGSF9BLRRN4CLQ8ND94393
IGSF9BRBM46Q8TBY0391
IGSF9BGRIN2BQ13224380
IGSF9BSLC32A1Q9H598378
IGSF9BDLX5P56178378

IntAct

7 interactions, top by confidence:

ABTypeScore
YAP1IGSF9Bpsi-mi:“MI:0407”(direct interaction)0.440
IGSF9BNEGR1psi-mi:“MI:0915”(physical association)0.400
Prdm16ESYT2psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (8): IGSF9B (Affinity Capture-RNA), IGSF9B (Affinity Capture-MS), IGSF9B (Affinity Capture-MS), IGSF9B (Protein-peptide), IGSF9B (Affinity Capture-MS), IGSF9B (Affinity Capture-MS), IGSF9B (Affinity Capture-MS), IGSF9B (Affinity Capture-MS)

ESM2 similar proteins: D3ZB51, E9PZ19, M0RAS4, O60242, O60245, O70472, O75882, O94779, P13590, P13591, P13595, P13596, P15209, P24786, P31836, P51641, P68500, P78539, P97300, P97527, P97546, Q01973, Q03351, Q15223, Q16288, Q16620, Q5IFJ9, Q5IS37, Q5IS82, Q63604, Q63769, Q6A051, Q6AZB0, Q6GQT9, Q6P1D5, Q6VNS1, Q7TNR6, Q80T74, Q80ZF8, Q8R4I7

Diamond homologs: A4FUY1, A6QQC6, A8MVW5, D3YXG0, D3ZB51, D3ZQE1, E9PZ19, O08775, P13595, P13596, P16573, P31809, P35968, P52583, Q00889, Q14CZ8, Q3KPI0, Q4VAH7, Q52KR2, Q62845, Q640R3, Q69Z26, Q9D2Z1, Q9HBG7, Q9UPX0, A2AJ76, A6NDA9, O55005, O75962, P0C6S8, Q1LUA6, Q3SXY7, Q3URE9, Q4R8Y9, Q504C1, Q6GQU6, Q6PFC5, Q7L985, Q80X72, Q8K099

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance3
Likely benign6
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
625595GRCh37/hg19 11q25(chr11:133325079-134157243)Pathogenic

SpliceAI

4842 predictions. Top by Δscore:

VariantEffectΔscore
11:133921394:CAAG:Cacceptor_gain1.0000
11:133921398:C:CCacceptor_gain1.0000
11:133922175:A:ACdonor_gain1.0000
11:133922176:C:CCdonor_gain1.0000
11:133922564:CCCA:Cdonor_loss1.0000
11:133922568:C:CAdonor_loss1.0000
11:133922589:CG:Cdonor_gain1.0000
11:133922726:GATGT:Gacceptor_gain1.0000
11:133922727:ATGT:Aacceptor_gain1.0000
11:133922728:TGT:Tacceptor_gain1.0000
11:133922729:GT:Gacceptor_gain1.0000
11:133922731:C:CAacceptor_loss1.0000
11:133922731:C:CCacceptor_gain1.0000
11:133924914:C:CTacceptor_gain1.0000
11:133925733:CCTCA:Cdonor_loss1.0000
11:133925734:CTCA:Cdonor_loss1.0000
11:133925735:TCAC:Tdonor_loss1.0000
11:133925736:CAC:Cdonor_loss1.0000
11:133925738:C:Gdonor_loss1.0000
11:133925766:T:Adonor_gain1.0000
11:133925961:GAATG:Gacceptor_gain1.0000
11:133925963:ATG:Aacceptor_gain1.0000
11:133925964:TG:Tacceptor_gain1.0000
11:133925964:TGC:Tacceptor_loss1.0000
11:133925966:C:CAacceptor_loss1.0000
11:133925966:C:CCacceptor_gain1.0000
11:133925970:G:Tacceptor_gain1.0000
11:133925972:C:CTacceptor_gain1.0000
11:133925973:G:Tacceptor_gain1.0000
11:133926912:TCACC:Tdonor_loss1.0000

AlphaMissense

9259 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:133922627:G:CS741R1.000
11:133922627:G:TS741R1.000
11:133922629:T:GS741R1.000
11:133922656:A:GC732R1.000
11:133924885:C:GR685P1.000
11:133925873:A:GW634R1.000
11:133925873:A:TW634R1.000
11:133926978:A:TV582D1.000
11:133926984:A:GF580S1.000
11:133929717:A:GW529R1.000
11:133929717:A:TW529R1.000
11:133930995:A:GL503P1.000
11:133931027:G:CN492K1.000
11:133931027:G:TN492K1.000
11:133931034:G:TA490D1.000
11:133931039:A:CC488W1.000
11:133931040:C:GC488S1.000
11:133931041:A:GC488R1.000
11:133931041:A:TC488S1.000
11:133931045:C:AW486C1.000
11:133931045:C:GW486C1.000
11:133931047:A:GW486R1.000
11:133931047:A:TW486R1.000
11:133931459:C:AW454C1.000
11:133931459:C:GW454C1.000
11:133931461:A:GW454R1.000
11:133931461:A:TW454R1.000
11:133931472:G:TP450H1.000
11:133931485:C:AG446W1.000
11:133931495:A:CC442W1.000

dbSNP variants (sampled 300 via entrez): RS1000047841 (11:133935404 C>T), RS1000081660 (11:133907032 C>G), RS1000113208 (11:133916409 G>A), RS1000148936 (11:133899044 C>A,G), RS1000171208 (11:133950107 G>A), RS1000229479 (11:133916098 C>T), RS1000309837 (11:133938354 C>T), RS1000338923 (11:133955147 G>A), RS1000341360 (11:133920591 A>G), RS1000368236 (11:133898877 G>A,C,T), RS1000511863 (11:133915392 C>CCAA), RS1000520319 (11:133934860 G>A,C), RS1000540056 (11:133951069 G>A), RS1000563541 (11:133917147 G>A,T), RS1000606851 (11:133949839 G>A)

Disease associations

OMIM: gene MIM:613773 | disease phenotypes: MIM:147791

GenCC curated gene-disease

Mondo (1): Jacobsen syndrome (MONDO:0007838)

Orphanet (1): Jacobsen syndrome (Orphanet:2308)

HPO phenotypes

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

GWAS associations

20 associations (top):

StudyTraitp-value
GCST001762_866Obesity-related traits1.000000e-06
GCST002539_12Schizophrenia4.000000e-11
GCST002981_3Longitudinal alcohol consumption5.000000e-07
GCST003720_11Migraine3.000000e-08
GCST004521_133Autism spectrum disorder or schizophrenia2.000000e-09
GCST004946_25Schizophrenia9.000000e-13
GCST005235_2Hand grip strength3.000000e-08
GCST006803_19Schizophrenia5.000000e-14
GCST006940_159Neurociticism3.000000e-08
GCST006950_6Feeling worry4.000000e-09
GCST007201_128Schizophrenia1.000000e-12
GCST007201_157Schizophrenia2.000000e-11
GCST008477_20Emphysema annual change measurement in smokers (adjusted lung density)9.000000e-06
GCST008522_4Bitter alcoholic beverage consumption3.000000e-08
GCST008595_112Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)2.000000e-10
GCST008757_39Alcohol consumption3.000000e-09
GCST009325_7Parkinson’s disease or first degree relation to individual with Parkinson’s disease6.000000e-20
GCST009600_134Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)6.000000e-10
GCST010988_508Adult body size2.000000e-10
GCST010991_12Parkinson’s disease7.000000e-09

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0005116urinary metabolite measurement
EFO:0007645longitudinal alcohol consumption measurement
EFO:0006941grip strength measurement
EFO:0007660neuroticism measurement
EFO:0009589worry measurement
EFO:0007626emphysema imaging measurement
EFO:0010092bitter alcoholic beverage consumption measurement
EFO:0004337intelligence
EFO:0004784self reported educational attainment

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases methylation2
Aflatoxin B1increases methylation2
FR900359increases phosphorylation1
Esketamineincreases expression1
triphenyl phosphateaffects expression1
mono-(2-ethylhexyl)phthalateincreases abundance, increases methylation1
sodium arseniteaffects methylation1
benzo(e)pyreneincreases methylation1
di-n-butylphosphoric acidaffects expression1
bisphenol Sdecreases methylation1
jinfukangaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, increases methylation1
Carbamazepineaffects expression1
Cisplatinincreases expression, affects cotreatment1
Diethylhexyl Phthalateincreases abundance, increases methylation1
Doxorubicindecreases expression1
Estradiolincreases expression1
Leadaffects expression1
Methapyrileneincreases methylation1
Silicon Dioxideincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Vanadiumincreases abundance, increases methylation1
Propofoldecreases expression1
Antirheumatic Agentsincreases expression1
Metals, Heavyincreases abundance, increases methylation1
Cadmium Chlorideincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04463316Not specifiedRECRUITINGGROWing Up With Rare GENEtic Syndromes
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Jacobsen syndrome, migraine disorder