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

    Gene ID: 286676, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (121987323..122061655, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (124707284..124781644, complement)
    RS_2024_09 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 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 autosomal recessive nonsyndromic hearing impairment locus (DFNB42) maps to chromosome 3q13.31-q22.3. Aslam M, et al. Am J Med Genet A, 2005 Feb 15. PMID 15641023, Free PMC Article
    3. A new recurrent chromosomal translocation t(3;11)(q13;q14) in myelodysplastic syndromes associated with overexpression of the ILDR1 gene. Zagaria A, et al. Leuk Res, 2012 Jul. PMID 22365942
    4. ILDR1: Novel mutation and a rare cause of congenital deafness in the Saudi Arabian population. Ramzan K, et al. Eur J Med Genet, 2014 May-Jun. PMID 24768815
    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
    		Compare labs

    EBI GWAS Catalog

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

    Variation

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    See Variation Viewer (GRCh37.p13)

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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_2024_08

    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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