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ILDR1 immunoglobulin like domain containing receptor 1 [ Homo sapiens (human) ]

Gene ID: 286676, updated on 11-Apr-2024

Summary

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Official Symbol
ILDR1provided by HGNC
Official Full Name
immunoglobulin like domain containing receptor 1provided by HGNC
Primary source
HGNC:HGNC:28741
See related
Ensembl:ENSG00000145103 MIM:609739; AllianceGenome:HGNC:28741
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DFNB42; ILDR1beta; ILDR1alpha; ILDR1alpha'
Summary
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]
Expression
Broad expression in colon (RPKM 3.8), prostate (RPKM 3.2) and 17 other tissues See more
Orthologs
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Genomic context

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See ILDR1 in Genome Data Viewer
Location:
3q13.33
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (121987323..122061655, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (124707284..124781644, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (121706170..121741094, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ELL associated factor 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:121611674-121612207 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:121612208-121612740 Neighboring gene solute carrier family 15 member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:121657363-121657943 Neighboring gene uncharacterized LOC101927010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:121711615-121712116 Neighboring gene Sharpr-MPRA regulatory region 6303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20352 Neighboring gene NANOG hESC enhancer GRCh37_chr3:121724759-121725260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14639 Neighboring gene CD86 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20365 Neighboring gene calcium sensing receptor Neighboring gene ReSE screen-validated silencer GRCh37_chr3:121983934-121984035 Neighboring gene NANOG hESC enhancer GRCh37_chr3:122026434-122026982 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 23

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Imputation of SNPs associated with presbycusis through linkage disequilibrium analysis in the ILDR1 gene. Flores SV, et al. J Genet, 2023. PMID 36814109
  2. 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. PMID 29849566, Free PMC Article
  3. 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, 2017. PMID 28945813, Free PMC Article
  4. Two novel mutations in ILDR1 gene cause autosomal recessive nonsyndromic hearing loss in consanguineous Iranian families. Mehrjoo Z, et al. J Genet, 2015 Sep. PMID 26440088
  5. 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. PMID 25668204, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Imputation of SNPs associated with presbycusis through linkage disequilibrium analysis in the ILDR1 gene.
    Title: Imputation of SNPs associated with presbycusis through linkage disequilibrium analysis in the ILDR1 gene.
  2. The study shows that the novel p.G141R mutation in ILDR1 is the likely genetic cause for the hearing impairment in two unrelated Chinese Han DFNB42 families.
    Title: A Novel p.G141R Mutation in ILDR1 Leads to Recessive Nonsyndromic Deafness DFNB42 in Two Chinese Han Families.
  3. this is the first ILDR1 and MYO6 mutations recognized in the southwest Iran. Our data expands the spectrum of mutations in ILDR1 and MYO6 genes.
    Title: 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.
  4. The present study reports a first ILDR1 gene mutation in a consanguineous family with hearing loss in the UAE, and confirms that the whole-exome sequencing approach is a robust tool for the diagnosis of monogenic diseases with high levels of allelic and locus heterogeneity.
    Title: Identification of a novel frameshift mutation in the ILDR1 gene in a UAE family, mutations review and phenotype genotype correlation.
  5. We discovered two genome-wide significant SNPs. The first was novel and near ISG20. The second was in TRIOBP, a gene previously associated with prelingual nonsyndromic hearing loss. Motivated by our TRIOBP results, we also looked at exons in known hearing loss genes, and identified two additional SNPs, rs2877561 in ILDR1 and rs9493672 in EYA4 (at a significance threshold adjusted for number of SNPs in those regions).
    Title: A Large Genome-Wide Association Study of Age-Related Hearing Impairment Using Electronic Health Records.
  6. consanguineous deaf families with novelmutations in the ILDR1 gene, were identified.
    Title: Two novel mutations in ILDR1 gene cause autosomal recessive nonsyndromic hearing loss in consanguineous Iranian families.
  7. Whole-exome sequencing of a Korean multiplex family segregating partial deafness identified a novel homozygous ILDR1 variant (p.P69H) within the Ig-like domain.
    Title: Downsloping high-frequency hearing loss due to inner ear tricellular tight junction disruption by a novel ILDR1 mutation in the Ig-like domain.
  8. Data indicate a mutation in immunoglobulin-like domain containing receptor 1 (ILDR1) as a causative gene for autosomal-recessive non-syndromic hearing loss (arNSHL) in a consanguineous Saudi family with three affected children.
    Title: ILDR1: Novel mutation and a rare cause of congenital deafness in the Saudi Arabian population.
  9. The findings show the heterogeneity of the molecular organization of tTJs in terms of the content of LSR, ILDR1 or ILDR2, and suggest that ILDR1-mediated recruitment of tricellulin to TCs is required for hearing.
    Title: Analysis of the 'angulin' proteins LSR, ILDR1 and ILDR2--tricellulin recruitment, epithelial barrier function and implication in deafness pathogenesis.
  10. The analysis of gene expression was extended to Refractory Anemia (RA) and Refractory Anemia with excess blasts (RAEB) cases revealing ILDR1 overexpression in 36% of RAEB subgroup.
    Title: A new recurrent chromosomal translocation t(3;11)(q13;q14) in myelodysplastic syndromes associated with overexpression of the ILDR1 gene.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive nonsyndromic hearing loss 42
MedGen: C1864818 OMIM: 609646 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of immunoglobulin-like domain containing receptor 1 (ILDR1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC50831

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables high-density lipoprotein particle receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables high-density lipoprotein particle receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
involved_in epithelial structure maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in establishment of localization in cell IEA
Inferred from Electronic Annotation
more info
  
involved_in peptide hormone secretion IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within positive regulation of peptide hormone secretion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein localization to tricellular tight junction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of RNA splicing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in response to fatty acid ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in tricellular tight junction assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in bicellular tight junction IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in tight junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in tricellular tight junction ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
immunoglobulin-like domain-containing receptor 1
Names
angulin-2
immunoglobulin-like domain-containing receptor 1 alpha
immunoglobulin-like domain-containing receptor 1 beta

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031870.2 RefSeqGene

    Range
    43308..78232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1377

mRNA and Protein(s)

  1. NM_001199799.2 → NP_001186728.1  immunoglobulin-like domain-containing receptor 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001186728.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK129974, AY672837, BC044240
    Consensus CDS
    CCDS56271.1
    UniProtKB/Swiss-Prot
    Q6ZP61, Q7Z578, Q86SU0
    Related
    ENSP00000345667.5, ENST00000344209.10
    Conserved Domains (1) summary
    cl11960
    Location:39 → 166
    Ig; Immunoglobulin domain

  2. NM_001199800.2 → NP_001186729.1  immunoglobulin-like domain-containing receptor 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001186729.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple exons in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC080098, AK129974, AY672839, BC044240
    Consensus CDS
    CCDS56270.1
    UniProtKB/Swiss-Prot
    Q86SU0
    Related
    ENSP00000377251.1, ENST00000393631.5

  3. NM_175924.4 → NP_787120.1  immunoglobulin-like domain-containing receptor 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_787120.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC080098, AK129974, BC044240
    Consensus CDS
    CCDS3008.1
    UniProtKB/Swiss-Prot
    Q86SU0
    Related
    ENSP00000273691.3, ENST00000273691.7
    Conserved Domains (1) summary
    cl11960
    Location:39 → 166
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    121987323..122061655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448044.1 → XP_047304000.1  immunoglobulin-like domain-containing receptor 1 isoform X4

  2. XM_047448043.1 → XP_047303999.1  immunoglobulin-like domain-containing receptor 1 isoform X3

  3. XM_011512738.3 → XP_011511040.1  immunoglobulin-like domain-containing receptor 1 isoform X1

    Conserved Domains (1) summary
    cl11960
    Location:39 → 166
    Ig; Immunoglobulin domain

  4. XM_005247389.5 → XP_005247446.1  immunoglobulin-like domain-containing receptor 1 isoform X2

    See identical proteins and their annotated locations for XP_005247446.1

    UniProtKB/Swiss-Prot
    Q86SU0
    Conserved Domains (1) summary
    PHA03307
    Location:307 → 511
    PHA03307; transcriptional regulator ICP4; Provisional

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    124707284..124781644 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346360.1 → XP_054202335.1  immunoglobulin-like domain-containing receptor 1 isoform X4

  2. XM_054346359.1 → XP_054202334.1  immunoglobulin-like domain-containing receptor 1 isoform X3

  3. XM_054346357.1 → XP_054202332.1  immunoglobulin-like domain-containing receptor 1 isoform X1

  4. XM_054346358.1 → XP_054202333.1  immunoglobulin-like domain-containing receptor 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86SU0.2 GenPept UniProtKB/Swiss-Prot:Q86SU0

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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