INAVA

innate immunity activator

Basic information

Region (hg38): 1:200891048-200915742

Previous symbols: [ "C1orf106" ]

Links

ENSG00000163362 ∙ NCBI:55765 ∙ OMIM:618051 ∙ HGNC:25599 ∙ Uniprot:Q3KP66 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INAVA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INAVA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			4	2	3	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	3	6

Variants in INAVA

This is a list of pathogenic ClinVar variants found in the INAVA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-200891603-G-A			Benign (Oct 17, 2017)
1-200891603-G-C			Benign (Mar 29, 2018)
1-200898444-T-A			Benign (Mar 01, 2023)
1-200899595-G-T		Inflammatory bowel disease 29	Uncertain significance (Jul 23, 2021)
1-200900111-C-T			Likely benign (Jun 27, 2018)
1-200900178-C-T			Benign (Jul 26, 2018)
1-200908890-C-A		not specified	Uncertain significance (Jun 18, 2021)
1-200908898-A-T		Inflammatory bowel disease 29	Uncertain significance (Jul 30, 2020)
1-200911573-G-A			Likely benign (Aug 01, 2022)
1-200911689-C-G		See cases	Likely benign (Apr 13, 2021)
1-200911751-G-A		not specified	Uncertain significance (Oct 14, 2021)
1-200911850-C-T			Benign (Dec 31, 2019)
1-200911898-C-T			Benign (Jul 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INAVA	protein_coding	protein_coding	ENST00000413687	9	24688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000221	0.996	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.368	349	369	0.946	0.0000254	3626
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000711	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.0000550	0.0000527
Middle Eastern	0.000711	0.000707
South Asian	0.0000662	0.0000653
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.662
• ghis: 0.431

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Inava
• Phenotype: skeleton phenotype

Gene ontology

• 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;response to muramyl dipeptide;positive regulation of interleukin-1 beta production;positive regulation of interleukin-10 production;positive regulation of interleukin-6 production;positive regulation of stress-activated MAPK cascade;adherens junction maintenance;positive regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;intestinal epithelial structure maintenance;nucleotide-binding oligomerization domain containing 2 signaling pathway;reactive oxygen species biosynthetic process
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding