IL11RA

interleukin 11 receptor subunit alpha, the group of Interleukin receptors|Immunoglobulin like domain containing

Basic information

Region (hg38): 9:34652161-34661902

Links

ENSG00000137070 ∙ NCBI:3590 ∙ OMIM:600939 ∙ HGNC:5967 ∙ Uniprot:Q14626 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• craniosynostosis and dental anomalies (Strong), mode of inheritance: AR
• craniosynostosis and dental anomalies (Moderate), mode of inheritance: AR
• craniosynostosis and dental anomalies (Strong), mode of inheritance: AR
• craniosynostosis and dental anomalies (Supportive), mode of inheritance: AR
• craniosynostosis and dental anomalies (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Craniosynostosis and dental anomalies	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental	21741611

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL11RA gene.

• not provided (62 variants)
• Craniosynostosis and dental anomalies (7 variants)
• not specified (4 variants)
• Craniosynostosis syndrome (1 variants)
• IL11RA-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL11RA 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				10	1	11
missense		4	16	2	5	27
nonsense	2					2
start loss		1				1
frameshift						0
inframe indel	1					1
splice donor/acceptor (+/-2bp)	1	1	1			3
splice region		1		1	2	4
non coding				5	17	22
Total	4	6	17	17	23

Highest pathogenic variant AF is 0.000118

Variants in IL11RA

This is a list of pathogenic ClinVar variants found in the IL11RA region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34654994-CGT-C			Benign (Dec 10, 2019)
9-34654994-C-CGT			Benign (Aug 26, 2019)
9-34654994-C-CGTGT			Likely benign (Jan 06, 2020)
9-34655016-T-TGTGC			Benign (Aug 15, 2019)
9-34655220-G-A			Likely pathogenic (Jul 01, 2017)
9-34655247-G-A			Likely benign (Oct 13, 2023)
9-34655277-G-A			Likely benign (Apr 01, 2022)
9-34655289-C-T		not specified	Benign/Likely benign (Dec 17, 2023)
9-34655294-G-GC		IL11RA-related disorder	Likely pathogenic (Dec 12, 2023)
9-34655316-A-C		IL11RA-related disorder	Likely benign (Oct 16, 2019)
9-34655439-T-C			Benign (Oct 16, 2018)
9-34655632-C-T		not specified	Benign/Likely benign (Jan 26, 2024)
9-34655657-G-C		IL11RA-related disorder	Likely benign (Dec 28, 2023)
9-34655663-C-T			Benign (Dec 06, 2023)
9-34655737-G-T			Benign (Oct 16, 2018)
9-34656482-G-A			Benign (Nov 10, 2018)
9-34656731-A-C			Benign (Jan 23, 2024)
9-34656737-A-T		IL11RA-related disorder	Likely pathogenic (May 03, 2023)
9-34656770-C-A		IL11RA-related disorder	Benign (Jan 02, 2024)
9-34656778-G-A			Likely benign (Dec 25, 2023)
9-34656846-G-A			Uncertain significance (Aug 22, 2022)
9-34656858-G-A			Uncertain significance (Aug 24, 2023)
9-34656858-G-T		Craniosynostosis and dental anomalies	Likely pathogenic (-)
9-34656883-G-A			Likely benign (Jan 27, 2022)
9-34656910-T-C		Craniosynostosis and dental anomalies	Uncertain significance (Dec 03, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL11RA	protein_coding	protein_coding	ENST00000555003	12	11191

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.29e-21	0.000445	125629	0	119	125748	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	209	237	0.883	0.0000147	2654
Missense in Polyphen		61	67.851	0.89903		828
Synonymous	0.121	95	96.5	0.984	0.00000539	933
Loss of Function	-0.607	29	25.7	1.13	0.00000141	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00153
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000423	0.000422
Middle Eastern	0.000381	0.000381
South Asian	0.000654	0.000653
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for interleukin-11. The receptor systems for IL6, LIF, OSM, CNTF, IL11 and CT1 can utilize IL6ST for initiating signal transmission. The IL11/IL11RA/IL6ST complex may be involved in the control of proliferation and/or differentiation of skeletogenic progenitor or other mesenchymal cells. Essential for the normal development of craniofacial bones and teeth. Restricts suture fusion and tooth number. {ECO:0000269|PubMed:21741611}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Interleukin-11 Signaling Pathway;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;Cytokine Signaling in Immune system;Immune System;IL11;Interleukin-6 family signaling (Consensus)

Recessive Scores

• pRec: 0.0877

Intolerance Scores

• loftool: 0.942
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.453
• hipred: N
• hipred_score: 0.173
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il11ra2

Gene ontology

• Biological process: positive regulation of cell population proliferation;cytokine-mediated signaling pathway;developmental process;interleukin-11-mediated signaling pathway;head development
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;receptor complex
• Molecular function: transmembrane signaling receptor activity;cytokine receptor activity;interleukin-11 receptor activity;cytokine binding;interleukin-11 binding