IL17RA

interleukin 17 receptor A, the group of CD molecules|Interleukin receptors

Basic information

Region (hg38): 22:17084953-17115693

Previous symbols: [ "IL17R" ]

Links

ENSG00000177663 ∙ NCBI:23765 ∙ OMIM:605461 ∙ HGNC:5985 ∙ Uniprot:Q96F46 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 51 (Limited), mode of inheritance: AR
• immunodeficiency 51 (Strong), mode of inheritance: AR
• chronic mucocutaneous candidiasis (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 51	AR	Allergy/Immunology/Infectious	Individuals have been described as susceptible to infections such as Candida albicans, Staphlycoccal skin infections, and bacterial respiratory infections, and awareness may allow early detection and early and aggressive treatment of infections	Allergy/Immunology/Infectious	21350122; 27930337

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL17RA gene.

• Immunodeficiency 51 (710 variants)
• Familial Candidiasis, Recessive (90 variants)
• Inborn genetic diseases (60 variants)
• not provided (24 variants)
• not specified (21 variants)
• See cases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL17RA 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			8	138	9	155
missense			306	8	8	322
nonsense	3		4			7
start loss						0
frameshift	5	1	3			9
inframe indel			5	1		6
splice donor/acceptor (+/-2bp)		3				3
splice region			17	19	2	38
non coding			129	67	55	251
Total	8	4	455	214	72

Highest pathogenic variant AF is 0.0000131

Variants in IL17RA

This is a list of pathogenic ClinVar variants found in the IL17RA region.

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

Position	Type	Phenotype	Significance	ClinVar
22-17084966-C-G		Immunodeficiency 51	Benign (Jan 13, 2018)
22-17084997-G-C		Immunodeficiency 51	Uncertain significance (Jan 12, 2018)
22-17084998-C-A		Familial Candidiasis, Recessive • not specified	Benign (Jan 24, 2024)
22-17085042-T-C		Familial Candidiasis, Recessive • not specified	Benign (Jan 24, 2024)
22-17085050-G-A		Immunodeficiency 51	Uncertain significance (Jan 12, 2018)
22-17085053-C-T		Immunodeficiency 51	Uncertain significance (Jan 12, 2018)
22-17085059-C-G		Immunodeficiency 51	Benign (Apr 27, 2017)
22-17085065-C-G		Immunodeficiency 51	Uncertain significance (Jan 13, 2018)
22-17085069-C-A		Immunodeficiency 51	Uncertain significance (Jan 13, 2018)
22-17085084-G-C		Familial Candidiasis, Recessive • not specified • Immunodeficiency 51	Benign (Jan 24, 2024)
22-17085086-C-G		IL17RA-related disorder	Likely benign (Nov 12, 2019)
22-17085099-C-T		Immunodeficiency 51	Uncertain significance (Aug 23, 2022)
22-17085100-C-A		Immunodeficiency 51	Likely benign (Dec 04, 2023)
22-17085104-C-T		Immunodeficiency 51	Uncertain significance (Feb 04, 2022)
22-17085108-G-A		Immunodeficiency 51	Uncertain significance (Jun 17, 2022)
22-17085108-G-C		not specified	Uncertain significance (May 23, 2023)
22-17085109-C-T		Immunodeficiency 51	Likely benign (Jun 15, 2023)
22-17085110-C-T		Immunodeficiency 51	Likely benign (Jan 08, 2024)
22-17085111-C-T		Familial Candidiasis, Recessive • Immunodeficiency 51 • IL17RA-related disorder	Likely benign (Jan 29, 2024)
22-17085114-C-T		Immunodeficiency 51	Uncertain significance (Feb 05, 2022)
22-17085117-C-T		Immunodeficiency 51	Uncertain significance (Sep 01, 2021)
22-17085121-T-A		Immunodeficiency 51 • IL17RA-related disorder	Conflicting classifications of pathogenicity (Jan 08, 2024)
22-17085124-C-A		Immunodeficiency 51	Likely benign (Sep 15, 2019)
22-17085127-G-T		Immunodeficiency 51	Conflicting classifications of pathogenicity (Aug 31, 2022)
22-17085132-C-G		Immunodeficiency 51	Uncertain significance (Jun 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL17RA	protein_coding	protein_coding	ENST00000319363	13	30740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000356	0.999	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.795	562	511	1.10	0.0000357	5559
Missense in Polyphen		133	144.26	0.92195		1854
Synonymous	-1.94	275	237	1.16	0.0000187	1778
Loss of Function	3.08	11	28.8	0.382	0.00000143	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000331	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000558	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for IL17A (PubMed:17911633, PubMed:9367539). Receptor for IL17F (PubMed:19838198, PubMed:17911633). Binds to IL17A with higher affinity than to IL17F (PubMed:17911633). Binds IL17A and IL17F homodimers as part of a heterodimeric complex with IL17RC (PubMed:16785495). Also binds heterodimers formed by IL17A and IL17F as part of a heterodimeric complex with IL17RC (PubMed:18684971). Receptor for IL17C as part of a heterodimeric complex with IL17RE (PubMed:21993848). Activation of IL17RA leads to induction of expression of inflammatory chemokines and cytokines such as CXCL1, CXCL8/IL8 and IL6 (PubMed:16785495, PubMed:17911633, PubMed:18684971). {ECO:0000269|PubMed:16785495, ECO:0000269|PubMed:17911633, ECO:0000269|PubMed:18684971, ECO:0000269|PubMed:19838198, ECO:0000269|PubMed:21993848, ECO:0000269|PubMed:9367539}.
• Disease: DISEASE: Immunodeficiency 51 (IMD51) [MIM:613953]: A primary immunodeficiency disorder with altered immune responses and impaired clearance of fungal infections, selective against Candida. It is characterized by persistent and/or recurrent infections of the skin, nails and mucous membranes caused by organisms of the genus Candida, mainly Candida albicans. {ECO:0000269|PubMed:21350122}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: IL-17 signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);IL17 signaling pathway;JAK STAT MolecularVariation 1;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.624
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.66

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.270
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il17ra
• Phenotype: hematopoietic system phenotype; neoplasm; respiratory 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;positive regulation of interleukin-23 production;defense response to fungus;granulocyte chemotaxis;fibroblast activation;interleukin-17-mediated signaling pathway;positive regulation of cytokine production involved in inflammatory response;positive regulation of interleukin-5 secretion;positive regulation of interleukin-13 secretion
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane
• Molecular function: signaling receptor binding;protein binding;interleukin-17 receptor activity