INAVA

protein-coding

innate immunity activator

Gene summary

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. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C1orf106

MANE transcript

NM_001142569.3

Inheritance

—

ClinVar variants

U:15B:7

Top phenotype

Inflammatory bowel disease 29

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr1:200,891,048-200,915,742

External References & Databases

Ensembl (ENSG00000163362)

Transcript & Mutation Effects

hg38 • Region Span ~24.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to INAVA variants in ClinVar

4 Conditions Cataloged

not providedTotal: 7

Inflammatory bowel disease 29Total: 4

not specifiedTotal: 2

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142569.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar	1 clinvar	6
missense			6 clinvar	3 clinvar	2 clinvar	11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	15	4	3	22

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142569.3	RefSeq	NP_001136041.1	9	MANE Select
ENST00000413687.3	Ensembl	ENSP00000392105.2	9	MANE Select
NM_001367289.1	RefSeq	NP_001354218.1	9	Standard
NM_001367290.1	RefSeq	NP_001354219.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

activation of MAPK activity
pattern recognition receptor signaling pathway
cytokine production involved in immune response
positive regulation of protein ubiquitination
response to peptidoglycan

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000413687
Coding exons: 9
Length: 24688
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125748
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.368	349	369	0.946	0.0000254	3626
Missense (PolyPhen)		102	108.2	0.94268		1003
Synonymous	0.422	144	151	0.956	0.00000969	1279
Loss of Function	2.53	10	23.1	0.432	0.00000123	253

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00071	0.00071	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: 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 (PubMed:28436939). 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 (PubMed:29420262). {ECO:0000269|PubMed:28436939, ECO:0000269|PubMed:29420262}.;
Disease: DISEASE: Note=Genetic variations in INAVA are associated with an increased risk of inflammatory bowel disease. A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology which is subdivided into Crohn disease and ulcerative colitis phenotypes. {ECO:0000269|PubMed:21983784, ECO:0000269|PubMed:28436939, ECO:0000269|PubMed:29420262}.;

Recessive Scores

pRec: 0.0972

Essentials

Essential (gene trap): N