ILDR1

immunoglobulin like domain containing receptor 1

Basic information

Region (hg38): 3:121987323-122022247

Previous symbols: [ "DFNB42" ]

Links

ENSG00000145103 ∙ NCBI:286676 ∙ OMIM:609739 ∙ HGNC:28741 ∙ Uniprot:Q86SU0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 42 (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 42 (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 42	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	15641023; 21255762; 23226338

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ILDR1 gene.

• Autosomal recessive nonsyndromic hearing loss 42 (5 variants)
• not provided (4 variants)
• Childhood onset hearing loss (1 variants)
• Rare genetic deafness (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILDR1 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			2	34	3	39
missense		1	105	3	7	116
nonsense	6	2				8
start loss						0
frameshift	3	3	1			7
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding			4	23	10	37
Total	9	6	112	60	20

Highest pathogenic variant AF is 0.0000263

Variants in ILDR1

This is a list of pathogenic ClinVar variants found in the ILDR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-121988101-C-CG			Likely benign (Jan 13, 2019)
3-121988356-G-A		not specified	Uncertain significance (Feb 05, 2018)
3-121988371-A-G			Uncertain significance (Oct 01, 2017)
3-121988395-G-C		Inborn genetic diseases	Uncertain significance (Aug 10, 2023)
3-121988418-A-G			Likely benign (Oct 18, 2022)
3-121988421-A-G		not specified	Likely benign (Oct 29, 2013)
3-121988423-A-AAT			Likely benign (Jun 16, 2021)
3-121992916-G-A			Benign (Nov 12, 2018)
3-121992919-G-A			Likely benign (Dec 23, 2018)
3-121993151-G-A			Uncertain significance (Jul 06, 2022)
3-121993155-G-A		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
3-121993167-T-C		not specified	Uncertain significance (Apr 28, 2015)
3-121993168-C-T		not specified • ILDR1-related disorder	Benign/Likely benign (Apr 01, 2024)
3-121993189-G-T		not specified	Conflicting classifications of pathogenicity (Jul 09, 2024)
3-121993204-A-C		not specified • Autosomal recessive nonsyndromic hearing loss 42	Benign (Jan 31, 2024)
3-121993212-G-A		not specified	Uncertain significance (Apr 17, 2017)
3-121993222-C-T			Likely benign (Nov 02, 2022)
3-121993223-G-A		not specified • Inborn genetic diseases	Uncertain significance (Jul 09, 2024)
3-121993233-C-T			Uncertain significance (Nov 27, 2023)
3-121993241-T-C		Inborn genetic diseases	Uncertain significance (Mar 07, 2023)
3-121993242-G-A			Uncertain significance (Jul 19, 2022)
3-121993245-G-C		Inborn genetic diseases	Uncertain significance (Nov 01, 2022)
3-121993251-G-A		not specified	Benign (Jan 29, 2024)
3-121993252-C-T			Likely benign (Aug 11, 2021)
3-121993258-G-A			Likely benign (Oct 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ILDR1	protein_coding	protein_coding	ENST00000344209	8	34882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-12	0.430	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.256	347	334	1.04	0.0000211	3528
Missense in Polyphen		138	141.32	0.9765		1484
Synonymous	-0.350	137	132	1.04	0.00000758	1093
Loss of Function	1.28	22	29.5	0.746	0.00000173	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000242
Ashkenazi Jewish	0.000307	0.000298
East Asian	0.000218	0.000217
Finnish	0.000511	0.000508
European (Non-Finnish)	0.000329	0.000325
Middle Eastern	0.000218	0.000217
South Asian	0.000589	0.000588
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative membrane receptor.

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.951
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.28

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.123
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ildr1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: ildr1b
• Affected structure: posterior lateral line primordium
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: receptor-mediated endocytosis;protein homooligomerization;positive regulation of peptide hormone secretion;cellular response to leukemia inhibitory factor
• Cellular component: cytosol;plasma membrane;integral component of membrane;protein-containing complex;tricellular tight junction
• Molecular function: identical protein binding;high-density lipoprotein particle receptor activity