ILDR1

Chr 3AR

immunoglobulin like domain containing receptor 1

Also known as: DFNB42, ILDR1alpha, ILDR1alpha', ILDR1beta

NCBI Gene: 286676ENSG00000145103UniProt: Q86SU0

This gene encodes a protein that contains an immunoglobulin-like domain. The encoded protein may function as a multimeric receptor at the cell surface. The expression of this gene may be a diagnostic marker for cancer progression. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

Primary Disease Associations & Inheritance

Deafness, autosomal recessive 42MIM #609646
AR
357
ClinVar variants
53
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— ILDR1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
53 Pathogenic / Likely Pathogenic· 177 VUS of 357 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.06LOEUF
pLI 0.000
Z-score 1.28
OE 0.75 (0.53–1.06)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.26Z-score
OE missense 1.04 (0.95–1.14)
347 obs / 333.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.75 (0.53–1.06)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.04 (0.95–1.14)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 22 / 29.5Missense obs/exp: 347 / 333.8Syn Z: -0.35

ClinVar Variant Classifications

357 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic36
Likely Pathogenic17
VUS177
Likely Benign81
Benign21
Conflicting17
36
Pathogenic
17
Likely Pathogenic
177
VUS
81
Likely Benign
21
Benign
17
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
7
1
28
0
36
Likely Pathogenic
10
3
4
0
17
VUS
1
162
13
1
177
Likely Benign
0
6
30
45
81
Benign
0
6
12
3
21
Conflicting
—17
Total181788749349

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ILDR1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

ILDR1-related deafness

definitive
ARLoss Of FunctionAbsent Gene Product
Ear
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Deafness, autosomal recessive 42

MIM #609646

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Next-generation sequencing identifies three novel missense variants in ILDR1 and MYO6 genes in an Iranian family with hearing loss with review of the literature.
Talebi F et al.·Int J Pediatr Otorhinolaryngol
2017Review
Mendelian non-syndromic and syndromic hearing loss genes contribute to presbycusis.
Cornejo-Sanchez DM et al.·Eur J Hum Genet
2025
ILDR1: Novel mutation and a rare cause of congenital deafness in the Saudi Arabian population.
Ramzan K et al.·Eur J Med Genet
2014
Downsloping high-frequency hearing loss due to inner ear tricellular tight junction disruption by a novel ILDR1 mutation in the Ig-like domain.
Kim NK et al.·PLoS One
2015
Genome-wide association meta-analysis identifies five novel loci for age-related hearing impairment.
Nagtegaal AP et al.·Sci Rep
2019Meta-analysis
Identification of a novel frameshift mutation in the ILDR1 gene in a UAE family, mutations review and phenotype genotype correlation.
Tlili A et al.·PLoS One
2017Review
Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis.
Aliazami F et al.·Int J Pediatr Otorhinolaryngol
2023Meta-analysis
Genomic analysis of childhood hearing loss in the Yoruba population of Nigeria.
Adeyemo A et al.·Eur J Hum Genet
2022
A Novel p.G141R Mutation in ILDR1 Leads to Recessive Nonsyndromic Deafness DFNB42 in Two Chinese Han Families.
Wang X et al.·Neural Plast
2018
Whole exome sequencing diagnosing syndromic and non-syndromic hearing loss with expansion of the phenotypic spectrum related to TMC1 variants.
Elbagoury NM et al.·Eur J Pediatr
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools