IL17C

interleukin 17C, the group of Interleukins

Basic information

Region (hg38): 16:88638572-88640468

Links

ENSG00000124391 ∙ NCBI:27189 ∙ OMIM:604628 ∙ HGNC:5983 ∙ Uniprot:Q9P0M4 ∙ 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 IL17C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL17C 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	1
missense			21	3	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	21	3	2

Variants in IL17C

This is a list of pathogenic ClinVar variants found in the IL17C region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88638646-C-T		not specified	Likely benign (Nov 07, 2022)
16-88639054-A-G		not specified	Uncertain significance (Sep 17, 2021)
16-88639068-G-A			Benign (Apr 24, 2018)
16-88639078-A-G		not specified	Likely benign (Aug 13, 2021)
16-88639107-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-88639120-C-A		not specified	Uncertain significance (Feb 16, 2023)
16-88639122-C-T		not specified	Uncertain significance (Nov 19, 2024)
16-88639180-G-A		not specified	Uncertain significance (Jun 06, 2023)
16-88639183-T-C		not specified	Uncertain significance (Dec 17, 2023)
16-88639228-C-T		not specified	Uncertain significance (Oct 26, 2024)
16-88639248-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-88639809-C-T			Likely benign (Aug 01, 2018)
16-88639867-T-C		not specified	Uncertain significance (Jun 06, 2023)
16-88639872-A-G		not specified	Uncertain significance (Oct 12, 2022)
16-88639881-A-G		not specified	Uncertain significance (Nov 30, 2022)
16-88639890-C-T		not specified	Uncertain significance (Nov 14, 2024)
16-88639926-C-T		not specified	Uncertain significance (Dec 27, 2023)
16-88639927-G-A		not specified	Uncertain significance (Aug 08, 2022)
16-88639954-G-A		not specified	Uncertain significance (Aug 20, 2024)
16-88639957-G-A		not specified	Uncertain significance (Mar 23, 2023)
16-88639959-C-T		not specified	Uncertain significance (Feb 27, 2024)
16-88639971-C-T		not specified	Uncertain significance (Sep 15, 2021)
16-88639972-G-A		not specified	Uncertain significance (Oct 26, 2021)
16-88639974-G-A		not specified	Uncertain significance (Aug 12, 2024)
16-88639977-G-A			Likely benign (May 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL17C	protein_coding	protein_coding	ENST00000244241	3	1883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000124	0.407	124303	0	30	124333	0.000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.811	156	130	1.20	0.00000823	1223
Missense in Polyphen		53	50.822	1.0429		446
Synonymous	-1.79	77	59.5	1.29	0.00000376	446
Loss of Function	0.135	6	6.37	0.942	3.16e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000269
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000557
Finnish	0.0000500	0.0000464
European (Non-Finnish)	0.000136	0.000133
Middle Eastern	0.0000557	0.0000557
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that plays a crucial role in innate immunity of the epithelium, including to intestinal bacterial pathogens, in an autocrine manner. Stimulates the production of antibacterial peptides and proinflammatory molecules for host defense by signaling through the NF-kappa-B and MAPK pathways. Acts synergically with IL22 in inducing the expression of antibacterial peptides, including S100A8, S100A9, REG3A and REG3G. Synergy is also observed with TNF and IL1B in inducing DEFB2 from keratinocytes. Depending on the type of insult, may have both protective and pathogenic properties, either by maintaining epithelial homeostasis after an inflammatory challenge or by promoting inflammatory phenotype. Enhanced IL17C/IL17RE signaling may also lead to greater susceptibility to autoimmune diseases. {ECO:0000269|PubMed:21993848}.
• Pathway: IL-17 signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);IL17 signaling pathway (Consensus)

Intolerance Scores

• loftool: 0.587
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.0968
• hipred: N
• hipred_score: 0.180
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.573

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Il17c
• Phenotype: hematopoietic system phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: inflammatory response;cell surface receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;interleukin-17-mediated signaling pathway
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity