INAVA

Summary

INAVA (innate immunity activator, HGNC:25599) is a protein-coding gene on chromosome 1q32.1, encoding Innate immunity activator protein (Q3KP66). Expressed in peripheral macrophages and intestinal myeloid-derived cells, is required for optimal PRR (pattern recognition receptor)-induced signaling, cytokine secretion, and bacterial clearance.

Involved in several processes, including nucleotide-binding activity oligomerization domain containing 2 signaling pathway; positive regulation of cytokine production; and positive regulation of intracellular signal transduction. Located in cytoplasm and nuclear body. Implicated in inflammatory bowel disease 29.

Source: NCBI Gene 55765 — RefSeq curated summary.

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 29 total
• Phenotypes (HPO): 4
• MANE Select transcript: NM_001142569

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25599
Approved symbol	INAVA
Name	innate immunity activator
Location	1q32.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10901
Ensembl gene	ENSG00000163362
Ensembl biotype	protein_coding
OMIM	618051
Entrez	55765

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 19 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000367342, ENST00000413687, ENST00000451872, ENST00000465162, ENST00000526172, ENST00000531649, ENST00000532631, ENST00000877560, ENST00000877561, ENST00000877562, ENST00000877563, ENST00000877564, ENST00000877565, ENST00000877566, ENST00000877567, ENST00000877568, ENST00000927410, ENST00000927411, ENST00000927412, ENST00000927413, ENST00000927414, ENST00000927415

RefSeq mRNA: 4 — MANE Select: NM_001142569 NM_001142569, NM_001367289, NM_001367290, NM_018265

CCDS: CCDS44292

Canonical transcript exons

ENST00000413687 — 10 exons

Exon	Start	End
ENSE00001073795	200911453	200912137
ENSE00001073797	200900937	200901159
ENSE00001073805	200899473	200899597
ENSE00001649654	200894900	200895087
ENSE00002147313	200913537	200915742
ENSE00002152049	200900104	200900220
ENSE00003488463	200898307	200898455
ENSE00003497734	200907834	200907887
ENSE00003533684	200908730	200908940
ENSE00003558809	200909224	200909397

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 98.64.

FANTOM5 (CAGE): breadth broad, TPM avg 5.2556 / max 156.2314, expressed in 703 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
7668	2.4161	318
7665	1.6896	509
7664	0.4272	203
7669	0.3122	139
7674	0.2149	119
7667	0.0722	40
7666	0.0714	33
7673	0.0347	7
7671	0.0104	6
7672	0.0069	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	98.64	gold quality
jejunal mucosa	UBERON:0000399	98.18	gold quality
nasal cavity epithelium	UBERON:0005384	97.63	gold quality
colonic mucosa	UBERON:0000317	97.12	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.78	gold quality
mucosa of transverse colon	UBERON:0004991	96.38	gold quality
lower esophagus mucosa	UBERON:0035834	96.16	gold quality
palpebral conjunctiva	UBERON:0001812	96.09	gold quality
pancreatic ductal cell	CL:0002079	95.87	gold quality
gingival epithelium	UBERON:0001949	95.80	gold quality
esophagus squamous epithelium	UBERON:0006920	95.49	gold quality
squamous epithelium	UBERON:0006914	95.06	gold quality
duodenum	UBERON:0002114	95.01	gold quality
upper leg skin	UBERON:0004262	94.90	gold quality
epithelium of esophagus	UBERON:0001976	94.74	gold quality
gingiva	UBERON:0001828	94.53	gold quality
upper arm skin	UBERON:0004263	93.92	gold quality
epithelium of bronchus	UBERON:0002031	93.78	gold quality
bronchial epithelial cell	CL:0002328	93.32	gold quality
bronchus	UBERON:0002185	93.31	gold quality
cervix squamous epithelium	UBERON:0006922	92.78	gold quality
nipple	UBERON:0002030	92.76	gold quality
pharyngeal mucosa	UBERON:0000355	92.65	gold quality
esophagus mucosa	UBERON:0002469	92.46	gold quality
skin of abdomen	UBERON:0001416	92.31	gold quality
zone of skin	UBERON:0000014	92.16	gold quality
skin of leg	UBERON:0001511	92.05	gold quality
tongue squamous epithelium	UBERON:0006919	91.35	gold quality
skin of hip	UBERON:0001554	91.19	gold quality
epithelium of nasopharynx	UBERON:0001951	91.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting INAVA, 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-5692A	100.00	74.40	6850
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-3913-5P	99.78	67.26	968
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-24-3P	99.59	69.97	1934

Literature-anchored findings (GeneRIF, showing 6)

• Results found that CpG sites of C1orf106, DMBX1, and SIK3 mediate the genetic risk of psoriasis in Chinese Han population. (PMID:27980695)
• IBD-associated polymorphisms in INAVA modulate PRR-initiated signaling, cytokines, and intracellular bacterial clearance, likely contributing to intestinal immune homeostasis. (PMID:28436939)
• C1orf106 regulates adherens junction stability by regulating the degradation of cytohesin-1, a guanine nucleotide exchange factor that controls activation of ARF6. (PMID:29420262)
• INAVA-CUPID exhibits dual functions, coordinated directly by ARNO, that bridge epithelial barrier function with extracellular signals and inflammation. (PMID:30355448)
• Study identifies C1ORF106 as an epithelial cell junction protein, and the loss of C1ORF106 augments TNF-alpha-induced intestinal epithelial leakage and diarrhea that may play a critical role in the development of inflammatory bowel disease. (PMID:31022698)
• Small-molecule modulators of INAVA cytosolic condensate and cell-cell junction assemblies. (PMID:34251416)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	inavab	ENSDARG00000070571
danio_rerio	inavaa	ENSDARG00000078155
mus_musculus	Inava	ENSMUSG00000041605
rattus_norvegicus	Inava	ENSRNOG00000025948

Paralogs (1): CCDC120 (ENSG00000147144)

Protein

Protein identifiers

Innate immunity activator protein — Q3KP66 (reviewed: Q3KP66)

All UniProt accessions (4): A0A8V8N8P9, C9JAT8, E9PK29, Q3KP66

UniProt curated annotations — full annotation on UniProt →

Function. Expressed in peripheral macrophages and intestinal myeloid-derived cells, is required for optimal PRR (pattern recognition receptor)-induced signaling, cytokine secretion, and bacterial clearance. Upon stimulation of a broad range of PRRs (pattern recognition receptor) such as NOD2 or TLR2, TLR3, TLR4, TLR5, TLR7 and TLR9, associates with YWHAQ/14-3-3T, which in turn leads to the recruitment and activation of MAP kinases and NF-kappa-B signaling complexes that amplifies PRR-induced downstream signals and cytokine secretion. In the intestine, regulates adherens junction stability by regulating the degradation of CYTH1 and CYTH2, probably acting as substrate cofactor for SCF E3 ubiquitin-protein ligase complexes. Stabilizes adherens junctions by limiting CYTH1-dependent ARF6 activation.

Subunit / interactions. Interacts with IRAK1, NOD2 and RIPK2; the interaction takes place upon PRR stimulation. Interacts with YWHAQ/14-3-3T; the interaction increases upon PRR stimulation and is required for cellular signaling pathway activation and cytokine secretion. Interacts (via N-terminal domain) with CYTH1 and CYTH2 (via their N-terminal domains). Interacts with FBXW11 and BTRC; associates with SCF E3 ubiquitin-protein ligase complexes.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Highly expressed in intestinal myeloid-derived cells and expressed in monocyte-derived macrophages upon induction by PRR activation.

Disease relevance. Inflammatory bowel disease 29 (IBD29) [MIM:618077] A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. Disease susceptibility is associated with variants affecting the gene represented in this entry.

Induction. Expression is induced by the component of peptidoglycan muramyl dipeptide. Negatively regulated by microRNA-24 (miR-24).

Isoforms (2)

UniProt ID	Names	Canonical?
Q3KP66-1	1	yes
Q3KP66-3	2

RefSeq proteins (4): NP_001136041, NP_001354218, NP_001354219, NP_060735 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021774	CUPID	Domain
IPR043447	CCDC120/INAVA	Family

Pfam: PF11819

UniProt features (25 total): compositionally biased region 6, mutagenesis site 6, region of interest 4, short sequence motif 3, sequence variant 2, chain 1, splice variant 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3KP66-F1	56.87	0.13

Functional residue map

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

Mutagenesis-validated functional residues (6):

Position	Phenotype
164–170	no effect on nuclear translocation upon induction by mdp. abolishes nuclear translocation upon induction by mdp and slig
246	decreases interaction with ywhaq, cellular signaling pathway activation and cytokine secretion.
335–338	no effect on nuclear translocation upon induction by mdp. abolishes nuclear translocation upon induction by mdp and slig
340	decreases interaction with ywhaq, cellular signaling pathway activation and cytokine secretion.
423–426	no effect on nuclear translocation upon induction by mdp. abolishes nuclear translocation upon induction by mdp and slig
616	decreases interaction with ywhaq, cellular signaling pathway activation and cytokine secretion.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 207 (showing top): GOBP_DIGESTION, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_REGULATION_OF_STRESS_ACTIVATED_PROTEIN_KINASE_SIGNALING_CASCADE, JAEGER_METASTASIS_DN, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_SIGNALING_PATHWAY, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, MAZ_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, YANG_BREAST_CANCER_ESR1_LASER_DN, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GOBP_CELLULAR_COMPONENT_MAINTENANCE, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP

GO Biological Process (17): pattern recognition receptor signaling pathway (GO:0002221), positive regulation of cytokine production involved in immune response (GO:0002720), positive regulation of protein ubiquitination (GO:0031398), response to peptidoglycan (GO:0032494), response to muramyl dipeptide (GO:0032495), positive regulation of interleukin-1 beta production (GO:0032731), positive regulation of interleukin-10 production (GO:0032733), positive regulation of interleukin-6 production (GO:0032755), positive regulation of stress-activated MAPK cascade (GO:0032874), adherens junction maintenance (GO:0034334), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), positive regulation of MAPK cascade (GO:0043410), innate immune response (GO:0045087), intestinal epithelial structure maintenance (GO:0060729), nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431), reactive oxygen species biosynthetic process (GO:1903409), immune system process (GO:0002376)

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

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of cytokine production	3
response to nitrogen compound	2
response to oxygen-containing compound	2
positive regulation of intracellular signal transduction	2
cellular anatomical structure	2
innate immune response-activating signaling pathway	1
cytokine production involved in immune response	1
positive regulation of production of molecular mediator of immune response	1
regulation of cytokine production involved in immune response	1
protein ubiquitination	1
regulation of protein ubiquitination	1
positive regulation of protein modification by small protein conjugation or removal	1
response to molecule of bacterial origin	1
interleukin-1 beta production	1
regulation of interleukin-1 beta production	1
positive regulation of interleukin-1 production	1
interleukin-10 production	1
regulation of interleukin-10 production	1
interleukin-6 production	1
regulation of interleukin-6 production	1
regulation of stress-activated MAPK cascade	1
positive regulation of MAPK cascade	1
stress-activated MAPK cascade	1
positive regulation of stress-activated protein kinase signaling cascade	1
adherens junction organization	1
cell-cell junction maintenance	1
canonical NF-kappaB signal transduction	1
regulation of canonical NF-kappaB signal transduction	1
MAPK cascade	1
regulation of MAPK cascade	1
immune response	1
defense response to symbiont	1
maintenance of gastrointestinal epithelium	1
nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway	1
biosynthetic process	1
reactive oxygen species metabolic process	1
biological_process	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Protein interactions and networks

STRING

506 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
INAVA	TRIM27	P14373	450
INAVA	GPR25	O00155	435
INAVA	KIF21B	O75037	419
INAVA	RNF186	Q9NXI6	403
INAVA	LRRC70	Q7Z2Q7	398
INAVA	CYTH1	Q15438	396
INAVA	SLC46A2	Q9BY10	371
INAVA	IL18RAP	O95256	368
INAVA	MUC19	Q7Z5P9	368
INAVA	NOD2	Q9HC29	353
INAVA	KBTBD11	O94819	349
INAVA	CYTH2	Q99418	348
INAVA	NPSR1	Q6W5P4	344
INAVA	CYTH4	Q9UIA0	343
INAVA	TMEM139	Q8IV31	324

IntAct

37 interactions, top by confidence:

A	B	Type	Score
PSMC3	PSMD9	psi-mi:“MI:0914”(association)	0.940
INAVA	CYTH1	psi-mi:“MI:0915”(physical association)	0.800
CYTH1	INAVA	psi-mi:“MI:0915”(physical association)	0.800
INAVA	CYTH2	psi-mi:“MI:0915”(physical association)	0.710
TAX1BP3	ARVCF	psi-mi:“MI:0914”(association)	0.690
INAVA	CYTH3	psi-mi:“MI:0914”(association)	0.640
INAVA	DCTN6	psi-mi:“MI:0914”(association)	0.530
PSME1	POLR3A	psi-mi:“MI:0914”(association)	0.530
ZNRD2	MYO9A	psi-mi:“MI:0914”(association)	0.530
PYCR3	RPL23	psi-mi:“MI:0914”(association)	0.530
CRP	QSOX1	psi-mi:“MI:0914”(association)	0.530
KCTD17	CBX4	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
BTRC	INAVA	psi-mi:“MI:0915”(physical association)	0.500
FBXW11	INAVA	psi-mi:“MI:0915”(physical association)	0.500
YWHAQ	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
INAVA	SFN	psi-mi:“MI:0915”(physical association)	0.400
ZNRD2	KRBA1	psi-mi:“MI:0914”(association)	0.350
PRPS2	ARHGEF37	psi-mi:“MI:0914”(association)	0.350
INAVA	ACACB	psi-mi:“MI:0914”(association)	0.350
VAC14	MGST3	psi-mi:“MI:0914”(association)	0.350
CAMK2D	PPM1D	psi-mi:“MI:0914”(association)	0.350
CREB3L2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
EFNB1	IPO5	psi-mi:“MI:0914”(association)	0.350

BioGRID (99): C1orf106 (Proximity Label-MS), CYTH2 (Affinity Capture-MS), CALCOCO2 (Affinity Capture-MS), CYTH1 (Affinity Capture-MS), CYTH3 (Affinity Capture-MS), PPP2R3B (Affinity Capture-MS), TAX1BP3 (Affinity Capture-MS), DCTN5 (Affinity Capture-MS), CRTAP (Affinity Capture-MS), DCTN6 (Affinity Capture-MS), CEP170 (Affinity Capture-MS), CCDC101 (Affinity Capture-MS), P3H1 (Affinity Capture-MS), ACTR10 (Affinity Capture-MS), ARHGEF7 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVZ6, A0JNN6, A2A9F4, A6NDZ8, A6NE82, A6NJ08, A6NJB7, A7MB40, A8MQ03, D2HS03, O43151, O93343, O94850, O95886, P01099, P97838, Q00587, Q0VBZ8, Q2KJ10, Q2M2S6, Q3KP66, Q58CU6, Q5NCP0, Q5RBE4, Q64322, Q68DV7, Q6AY88, Q6PFD5, Q7TN12, Q80V38, Q86YN6, Q86YV5, Q8BFY7, Q8BG87, Q8NAX2, Q8NC06, Q8NHZ7, Q8TEF2, Q91XA5, Q96EL1

Diamond homologs: A2AEV7, Q3KP66, Q7TN12, Q920B0, Q96HB5, Q9Y2L6, Q8BIE6, Q9P2Q2, P26038, P26042, Q2HJ49, P26040, P31977, Q8HZQ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	3
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

1264 predictions. Top by Δscore:

Variant	Effect	Δscore
1:200898451:GTCTG:G	donor_gain	1.0000
1:200898452:TCTG:T	donor_gain	1.0000
1:200898456:G:GA	donor_loss	1.0000
1:200898456:G:GG	donor_gain	1.0000
1:200899468:TGCA:T	acceptor_loss	1.0000
1:200899469:GCAG:G	acceptor_loss	1.0000
1:200899470:CA:C	acceptor_loss	1.0000
1:200899471:A:AG	acceptor_gain	1.0000
1:200899472:G:GG	acceptor_gain	1.0000
1:200899592:G:GT	donor_gain	1.0000
1:200899592:G:T	donor_gain	1.0000
1:200899595:GCG:G	donor_gain	1.0000
1:200900102:A:AG	acceptor_gain	1.0000
1:200900103:G:GG	acceptor_gain	1.0000
1:200900216:GAGAG:G	donor_gain	1.0000
1:200900218:GAG:G	donor_gain	1.0000
1:200900221:GTG:G	donor_loss	1.0000
1:200900222:T:G	donor_loss	1.0000
1:200900934:CAG:C	acceptor_loss	1.0000
1:200900935:A:AG	acceptor_gain	1.0000
1:200900935:AG:A	acceptor_gain	1.0000
1:200900935:AGG:A	acceptor_loss	1.0000
1:200900936:G:GG	acceptor_gain	1.0000
1:200900936:GG:G	acceptor_gain	1.0000
1:200900936:GGA:G	acceptor_gain	1.0000
1:200900936:GGAC:G	acceptor_gain	1.0000
1:200900936:GGACC:G	acceptor_gain	1.0000
1:200901156:CGAGG:C	donor_loss	1.0000
1:200901157:GAG:G	donor_gain	1.0000
1:200901158:AGGTG:A	donor_loss	1.0000

AlphaMissense

3686 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:200912004:T:C	L589P	0.995
1:200912014:G:C	W592C	0.995
1:200912014:G:T	W592C	0.995
1:200899595:G:C	A145P	0.994
1:200900983:T:C	I200T	0.994
1:200912004:T:A	L589H	0.994
1:200912012:T:A	W592R	0.994
1:200912012:T:C	W592R	0.994
1:200900991:G:C	A203P	0.993
1:200900983:T:G	I200S	0.989
1:200900994:G:C	A204P	0.989
1:200901046:G:C	R221P	0.988
1:200908870:T:A	W324R	0.988
1:200908870:T:C	W324R	0.988
1:200900108:T:C	L147P	0.987
1:200907854:A:C	S266R	0.987
1:200907856:C:A	S266R	0.987
1:200907856:C:G	S266R	0.987
1:200909342:A:C	S387R	0.985
1:200909344:T:A	S387R	0.985
1:200909344:T:G	S387R	0.985
1:200899572:T:C	L137P	0.984
1:200901079:T:C	L232P	0.983
1:200912013:G:C	W592S	0.982
1:200900114:G:T	G149V	0.981
1:200900175:G:C	R169S	0.981
1:200900175:G:T	R169S	0.981
1:200899585:C:G	C141W	0.979
1:200899590:G:C	R143P	0.979
1:200908872:G:C	W324C	0.977

dbSNP variants (sampled 300 via entrez): RS1000059611 (1:200894242 G>C), RS1000243829 (1:200897374 A>G), RS1000307818 (1:200897559 A>G), RS1000326230 (1:200905429 A>G), RS1000336809 (1:200899269 G>A), RS1000480249 (1:200915954 A>G), RS1000603309 (1:200915838 C>A), RS1000965919 (1:200907538 G>C), RS1001152774 (1:200901449 C>G), RS1001164479 (1:200909238 C>T), RS1001220789 (1:200910723 A>C), RS1001238545 (1:200914201 C>T), RS1001436553 (1:200897919 G>T), RS1001446861 (1:200907793 T>C), RS1001508588 (1:200898307 C>A,G)

Disease associations

OMIM: gene MIM:618051 | disease phenotypes: MIM:618077

GenCC curated gene-disease

Mondo (1): inflammatory bowel disease 29 (MONDO:0054849)

Orphanet (0):

HPO phenotypes

4 total (4 of 4 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0003829	Typified by incomplete penetrance
HP:0100279	Ulcerative colitis
HP:0100280	Crohn’s disease

GWAS associations

20 associations (top):

Study	Trait	p-value
GCST000879_25	Crohn’s disease	2.000000e-07
GCST000964_17	Ulcerative colitis	2.000000e-13
GCST001198_6	Multiple sclerosis	2.000000e-09
GCST004131_38	Inflammatory bowel disease	1.000000e-21
GCST004132_68	Crohn’s disease	1.000000e-10
GCST004133_18	Ulcerative colitis	4.000000e-16
GCST005523_6	Celiac disease	3.000000e-08
GCST005531_104	Multiple sclerosis	4.000000e-19
GCST005537_148	Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)	5.000000e-41
GCST007362_4	Acute anterior uveitis (with or without ankylosing spondylitis)	2.000000e-07
GCST008489_3	Celiac disease	3.000000e-08
GCST009597_302	Multiple sclerosis	6.000000e-21
GCST009874_28	Celiac disease	8.000000e-09
GCST010697_41	Cortical surface area (min-P)	2.000000e-21
GCST010698_48	Subcortical volume (min-P)	4.000000e-11
GCST010699_65	Brain morphology (min-P)	2.000000e-23
GCST010700_61	Cortical thickness (MOSTest)	2.000000e-09
GCST010701_90	Cortical surface area (MOSTest)	4.000000e-14
GCST010702_100	Subcortical volume (MOSTest)	2.000000e-08
GCST010703_156	Brain morphology (MOSTest)	3.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression	5
trichostatin A	affects cotreatment, decreases expression	3
(+)-JQ1 compound	decreases expression	3
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression, affects expression, increases expression	3
sodium arsenite	decreases expression, increases abundance, increases expression, affects cotreatment	2
perfluorooctane sulfonic acid	decreases expression, increases expression	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
FR900359	decreases phosphorylation	1
terbufos	increases methylation	1
sulforaphane	decreases expression	1
butyraldehyde	decreases expression	1
aflatoxin B2	decreases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Decitabine	increases expression	1
Leflunomide	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Caffeine	decreases phosphorylation	1
Calcitriol	increases expression	1
Cisplatin	increases expression	1
Fonofos	increases methylation	1
Hydralazine	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1
Methyl Methanesulfonate	decreases expression	1

Clinical trials (associated diseases)

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