IGSF22

Summary

IGSF22 (immunoglobulin superfamily member 22, HGNC:26750) is a protein-coding gene on chromosome 11p15.1, encoding Immunoglobulin superfamily member 22 (Q8N9C0).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 205 total
• MANE Select transcript: NM_173588

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26750
Approved symbol	IGSF22
Name	immunoglobulin superfamily member 22
Location	11p15.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37794, IGFN2
Ensembl gene	ENSG00000179057
Ensembl biotype	protein_coding
Entrez	283284

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding

ENST00000319338, ENST00000412229, ENST00000504981, ENST00000510673, ENST00000513874

RefSeq mRNA: 1 — MANE Select: NM_173588 NM_173588

CCDS: CCDS41625

Canonical transcript exons

ENST00000513874 — 23 exons

Exon	Start	End
ENSE00001220297	18710327	18710455
ENSE00001220302	18710655	18710828
ENSE00002032667	18704312	18704538
ENSE00002075256	18726074	18726188
ENSE00003461539	18724128	18724269
ENSE00003479157	18714277	18714418
ENSE00003489911	18713852	18714148
ENSE00003501786	18718615	18718728
ENSE00003521020	18709387	18709683
ENSE00003529622	18715432	18715716
ENSE00003557678	18707804	18707996
ENSE00003559794	18708207	18708295
ENSE00003560439	18721910	18722041
ENSE00003560867	18712082	18712384
ENSE00003596016	18720064	18720103
ENSE00003600156	18717931	18718093
ENSE00003602604	18706914	18707213
ENSE00003611489	18721535	18721671
ENSE00003621213	18705817	18706146
ENSE00003628718	18720186	18720285
ENSE00003633152	18719716	18719893
ENSE00003646155	18716728	18717000
ENSE00003679604	18714500	18714624

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 82.75.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0217 / max 13.5666, expressed in 7 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118957	0.0217	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	82.75	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.73	gold quality
skin of abdomen	UBERON:0001416	79.86	gold quality
zone of skin	UBERON:0000014	79.42	gold quality
lower esophagus mucosa	UBERON:0035834	79.03	gold quality
adrenal tissue	UBERON:0018303	77.53	gold quality
buccal mucosa cell	CL:0002336	77.12	gold quality
nucleus accumbens	UBERON:0001882	76.10	gold quality
pituitary gland	UBERON:0000007	74.63	gold quality
adenohypophysis	UBERON:0002196	74.12	gold quality
tendon of biceps brachii	UBERON:0008188	74.03	silver quality
right frontal lobe	UBERON:0002810	73.92	gold quality
right lobe of thyroid gland	UBERON:0001119	73.84	gold quality
anterior cingulate cortex	UBERON:0009835	73.81	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.69	gold quality
putamen	UBERON:0001874	73.61	gold quality
left lobe of thyroid gland	UBERON:0001120	73.56	gold quality
metanephros cortex	UBERON:0010533	72.88	gold quality
thyroid gland	UBERON:0002046	72.76	gold quality
hypothalamus	UBERON:0001898	72.65	gold quality
endothelial cell	CL:0000115	72.57	silver quality
caudate nucleus	UBERON:0001873	72.38	gold quality
left ovary	UBERON:0002119	72.35	gold quality
prefrontal cortex	UBERON:0000451	72.33	gold quality
right ovary	UBERON:0002118	72.28	gold quality
gall bladder	UBERON:0002110	72.07	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	71.76	gold quality
apex of heart	UBERON:0002098	71.73	gold quality
adult mammalian kidney	UBERON:0000082	70.95	gold quality
right hemisphere of cerebellum	UBERON:0014890	70.95	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting IGSF22, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-2467-3P	98.65	67.18	1969

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	igfn1.1	ENSDARG00000005526
danio_rerio	igfn1.2	ENSDARG00000075926
danio_rerio	igfn1.4	ENSDARG00000086028
danio_rerio	igfn1.3	ENSDARG00000097613

Paralogs (11): MYOM2 (ENSG00000036448), FNDC3B (ENSG00000075420), MYBPC2 (ENSG00000086967), MYOM1 (ENSG00000101605), FNDC3A (ENSG00000102531), OBSL1 (ENSG00000124006), MYBPH (ENSG00000133055), MYBPC3 (ENSG00000134571), MYOM3 (ENSG00000142661), MYBPC1 (ENSG00000196091), MYBPHL (ENSG00000221986)

Protein

Protein identifiers

Immunoglobulin superfamily member 22 — Q8N9C0 (reviewed: Q8N9C0)

All UniProt accessions (1): Q8N9C0

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N9C0-1	1	yes
Q8N9C0-2	2

RefSeq proteins (1): NP_775859* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR040849	MyBP-C_THB	Domain
IPR050964	Striated_Muscle_Regulatory	Family

Pfam: PF00041, PF07679, PF18362

UniProt features (20 total): sequence variant 8, domain 6, sequence conflict 3, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9C0-F1	85.34	0.62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): USF_C, PAX8_B, MYCMAX_01, USF_01, TCF11_01, IK2_01, USF_02, AP1FJ_Q2, USF2_Q6, ATCTTGC_MIR31, MYC_Q2, MAX_01, ARNT_01, DODD_NASOPHARYNGEAL_CARCINOMA_DN, AR_Q6

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

746 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IGSF22	SSX7	Q7RTT5	584
IGSF22	SSX5	O60225	511
IGSF22	CCDC90B	Q9GZT6	487
IGSF22	IGSF21	Q96ID5	452
IGSF22	SSX3	Q99909	447
IGSF22	IGSF3	O75054	404
IGSF22	SEL1L3	Q68CR1	401
IGSF22	CCDC43	Q96MW1	400
IGSF22	IGSF1	Q8N6C5	400
IGSF22	IGSF6	O95976	398
IGSF22	IGSF5	Q9NSI5	396
IGSF22	CCDC171	Q6TFL3	384
IGSF22	IL9	P15248	378
IGSF22	IL13	P35225	376
IGSF22	CCL5	P13501	375
IGSF22	IL17A	Q16552	375

IntAct

2 interactions, top by confidence:

A	B	Type	Score
IGSF22	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (3): IGF2R (Cross-Linking-MS (XL-MS)), NDUFA9 (Cross-Linking-MS (XL-MS)), IGSF22 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WV53, A2AAJ9, A2ABU4, A2RUH7, E7F6H7, O00423, O01761, O14576, O54785, O70468, O88485, O88599, P16419, P22607, P26453, P52179, P53670, P53671, P54296, P56741, P70402, Q00872, Q02173, Q05623, Q05BC3, Q0DYP5, Q13203, Q14168, Q14324, Q14896, Q29RQ3, Q32L23, Q4V8C3, Q5FW53, Q5PQM4, Q5VST9, Q5VTT5, Q5XI81, Q5XKE0, Q60992

Diamond homologs: A0A087WV53, A2ASS6, A2CG49, A2RUH7, F1M0Z1, O08775, O60229, O70468, O75962, O88599, O94856, P11799, P16419, P35918, P56741, P70402, P97685, P97924, Q00872, Q05623, Q0KL02, Q13203, Q14324, Q14896, Q15746, Q5FW53, Q5PQM4, Q5VTT5, Q5XKE0, Q63518, Q696W0, Q6GMZ9, Q7T2H2, Q8N9C0, Q8WZ42, Q90688, Q9JIF9, A2ASQ1, A3KN33, A8DYP0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	186
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4047 predictions. Top by Δscore:

Variant	Effect	Δscore
11:18706144:GGACT:G	acceptor_loss	1.0000
11:18706147:C:CC	acceptor_gain	1.0000
11:18706147:CT:C	acceptor_loss	1.0000
11:18706907:GACT:G	donor_loss	1.0000
11:18706908:ACT:A	donor_loss	1.0000
11:18706909:CT:C	donor_loss	1.0000
11:18706910:T:TG	donor_loss	1.0000
11:18706911:CAC:C	donor_loss	1.0000
11:18706912:A:AC	donor_gain	1.0000
11:18706912:A:C	donor_loss	1.0000
11:18706912:ACT:A	donor_gain	1.0000
11:18706913:C:CA	donor_gain	1.0000
11:18706913:CT:C	donor_gain	1.0000
11:18706913:CTC:C	donor_gain	1.0000
11:18706913:CTCT:C	donor_gain	1.0000
11:18706913:CTCTG:C	donor_gain	1.0000
11:18706919:T:TA	donor_gain	1.0000
11:18706924:A:AC	donor_gain	1.0000
11:18706961:CTG:C	donor_gain	1.0000
11:18706962:TGT:T	donor_gain	1.0000
11:18707004:T:TA	donor_gain	1.0000
11:18707214:C:CC	acceptor_gain	1.0000
11:18707214:CTGGA:C	acceptor_loss	1.0000
11:18707215:T:A	acceptor_loss	1.0000
11:18708205:A:AC	donor_gain	1.0000
11:18708206:C:CC	donor_gain	1.0000
11:18709684:C:CC	acceptor_gain	1.0000
11:18710325:A:AC	donor_gain	1.0000
11:18710326:C:CC	donor_gain	1.0000
11:18710326:CTAA:C	donor_gain	1.0000

AlphaMissense

8766 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:18716817:A:G	L386P	1.000
11:18709464:C:G	R873P	0.999
11:18710388:A:C	N779K	0.999
11:18710388:A:T	N779K	0.999
11:18710404:C:G	R774P	0.999
11:18710407:A:G	F773S	0.999
11:18713895:A:C	N684K	0.999
11:18713895:A:T	N684K	0.999
11:18713953:A:G	L665P	0.999
11:18714026:A:G	W641R	0.999
11:18714026:A:T	W641R	0.999
11:18714328:A:C	Y583D	0.999
11:18714366:A:G	L570P	0.999
11:18714520:A:G	W546R	0.999
11:18714520:A:T	W546R	0.999
11:18715501:A:C	Y488D	0.999
11:18715539:A:G	L475P	0.999
11:18715612:A:G	W451R	0.999
11:18715612:A:T	W451R	0.999
11:18716739:A:G	L412P	0.999
11:18716896:A:G	W360R	0.999
11:18716896:A:T	W360R	0.999
11:18717942:A:G	L321P	0.999
11:18717982:A:C	Y308D	0.999
11:18718020:A:G	L295P	0.999
11:18718623:A:G	W268R	0.999
11:18718623:A:T	W268R	0.999
11:18721539:A:G	L125P	0.999
11:18721613:C:A	W100C	0.999
11:18721613:C:G	W100C	0.999

dbSNP variants (sampled 300 via entrez): RS1000002455 (11:18713766 G>C), RS1000029786 (11:18717364 A>C), RS1000033826 (11:18713951 T>C), RS1000161450 (11:18719513 C>T), RS1000306632 (11:18726244 T>C), RS1000358590 (11:18726400 G>A), RS1000724287 (11:18706153 G>A,C), RS1000884315 (11:18712685 G>C), RS1001042095 (11:18715005 C>T), RS1001070876 (11:18718519 T>A), RS1001103026 (11:18708581 T>C), RS1001130191 (11:18725980 C>T), RS1001155316 (11:18705859 C>T), RS1001417261 (11:18714695 G>A,C), RS1001438714 (11:18718964 T>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003098_15	Diabetic kidney disease	5.000000e-06
GCST010002_232	Refractive error	2.000000e-27

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
fluorene-9-bisphenol	decreases expression	1
propionaldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
abrine	increases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Lead	affects expression	1
Lipopolysaccharides	increases expression, decreases expression, affects response to substance	1
Naphthoquinones	increases expression	1

Clinical trials (associated diseases)

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