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EDA ectodysplasin A [ Homo sapiens (human) ]

Gene ID: 1896, updated on 3-Apr-2024

Summary

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Official Symbol
EDAprovided by HGNC
Official Full Name
ectodysplasin Aprovided by HGNC
Primary source
HGNC:HGNC:3157
See related
Ensembl:ENSG00000158813 MIM:300451; AllianceGenome:HGNC:3157
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
ED1; HED; EDA1; EDA2; HED1; ODT1; XHED; ECTD1; XLHED; ED1-A1; ED1-A2; EDA-A1; EDA-A2; TNLG7C; STHAGX1
Summary
The protein encoded by this gene is a type II membrane protein that can be cleaved by furin to produce a secreted form. The encoded protein, which belongs to the tumor necrosis factor family, acts as a homotrimer and may be involved in cell-cell signaling during the development of ectodermal organs. Defects in this gene are a cause of ectodermal dysplasia, anhidrotic, which is also known as X-linked hypohidrotic ectodermal dysplasia. Several transcript variants encoding many different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in adrenal (RPKM 1.8), thyroid (RPKM 1.7) and 24 other tissues See more
Orthologs
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Genomic context

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See EDA in Genome Data Viewer
Location:
Xq13.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (69616113..70039472)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (68049526..68472825)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (68835957..69259322)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chrX:68725122-68725295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:68726227-68726726 Neighboring gene CYCS pseudogene 43 Neighboring gene NALCN channel auxiliary factor 2 Neighboring gene MPRA-validated peak7391 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20888 Neighboring gene uncharacterized LOC124905293 Neighboring gene RNA, 5S ribosomal pseudogene 506 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:68925458-68926249 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:69058411-69058611 Neighboring gene PRKX pseudogene 2 Neighboring gene CCR4-NOT transcription complex subunit 7 pseudogene 1 Neighboring gene microRNA 676 Neighboring gene acyl-CoA wax alcohol acyltransferase 2 Neighboring gene OTU deubiquitinase 6A

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. Association between Circulating Ectodysplasin A and Diabetic Kidney Disease. Deng X, et al. J Diabetes Res, 2023. PMID 37091044, Free PMC Article
  2. A novel deletion of exon 4 in the Ectodysplasin A gene associated with X-linked hypohidrotic ectodermal dysplasia. Agiannitopoulos K, et al. Arch Oral Biol, 2023 Jun. PMID 37001412
  3. Structural insights into pathogenic mechanism of hypohidrotic ectodermal dysplasia caused by ectodysplasin A variants. Yu K, et al. Nat Commun, 2023 Feb 11. PMID 36765055, Free PMC Article
  4. A novel mutation in the collagen domain of EDA results in hypohidrotic ectodermal dysplasia by impacting the receptor-binding capability. Liu X, et al. Mol Genet Genomic Med, 2023 Apr. PMID 36448232, Free PMC Article
  5. Two Novel Mutations in Ectodysplasin-A Identified in Syndromic Tooth Agenesis. Xie W, et al. J Coll Physicians Surg Pak, 2022 May. PMID 35546689

See all (138) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identified a novel splicing mutation at EDA gene in a hypohidrotic ectodermal dysplasia pedigree.
    Title: Identified a novel splicing mutation at EDA gene in a hypohidrotic ectodermal dysplasia pedigree.
  2. Association between Circulating Ectodysplasin A and Diabetic Kidney Disease.
    Title: Association between Circulating Ectodysplasin A and Diabetic Kidney Disease.
  3. A novel deletion of exon 4 in the Ectodysplasin A gene associated with X-linked hypohidrotic ectodermal dysplasia.
    Title: A novel deletion of exon 4 in the Ectodysplasin A gene associated with X-linked hypohidrotic ectodermal dysplasia.
  4. A novel mutation in the collagen domain of EDA results in hypohidrotic ectodermal dysplasia by impacting the receptor-binding capability.
    Title: A novel mutation in the collagen domain of EDA results in hypohidrotic ectodermal dysplasia by impacting the receptor-binding capability.
  5. Structural insights into pathogenic mechanism of hypohidrotic ectodermal dysplasia caused by ectodysplasin A variants.
    Title: Structural insights into pathogenic mechanism of hypohidrotic ectodermal dysplasia caused by ectodysplasin A variants.
  6. Ectodysplasin-A mRNA in exosomes released from activated hepatic stellate cells stimulates macrophage response.
    Title: Ectodysplasin-A mRNA in exosomes released from activated hepatic stellate cells stimulates macrophage response.
  7. Two Novel Mutations in Ectodysplasin-A Identified in Syndromic Tooth Agenesis.
    Title: Two Novel Mutations in Ectodysplasin-A Identified in Syndromic Tooth Agenesis.
  8. Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India.
    Title: Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India.
  9. Two novel ectodysplasin A gene mutations and prenatal diagnosis of X-linked hypohidrotic ectodermal dysplasia.
    Title: Two novel ectodysplasin A gene mutations and prenatal diagnosis of X-linked hypohidrotic ectodermal dysplasia.
  10. Understanding the impact of missense mutations on the structure and function of the EDA gene in X-linked hypohidrotic ectodermal dysplasia: A bioinformatics approach.
    Title: Understanding the impact of missense mutations on the structure and function of the EDA gene in X-linked hypohidrotic ectodermal dysplasia: A bioinformatics approach.
Submit: New GeneRIF Correction See all GeneRIFs (97)

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
Hypohidrotic X-linked ectodermal dysplasia
MedGen: C0162359 OMIM: 305100 GeneReviews: Hypohidrotic Ectodermal Dysplasia
Compare labs
Tooth agenesis, selective, X-linked, 1
MedGen: C1970757 OMIM: 313500 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2023-01-25)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2023-01-25)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
EBI GWAS Catalog
Genome-wide association study reveals multiple loci associated with primary tooth development during infancy.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables death receptor agonist activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables death receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables tumor necrosis factor receptor binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in animal organ development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in hair follicle placode formation IEA
Inferred from Electronic Annotation
more info
  
involved_in immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in odontogenesis of dentin-containing tooth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in pigmentation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of non-canonical NF-kappaB signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in salivary gland cavitation IEA
Inferred from Electronic Annotation
more info
  
involved_in trachea gland development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in apical part of cell IEA
Inferred from Electronic Annotation
more info
  
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton TAS
Traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in lipid droplet IDA
Inferred from Direct Assay
more info
  
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ectodysplasin-A
Names
X-linked anhidroitic ectodermal dysplasia protein
oligodontia 1
tumor necrosis factor ligand 7C

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_009809.2 RefSeqGene

    Range
    5047..428406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005609.2 → NP_001005609.1  ectodysplasin-A isoform 2

    See identical proteins and their annotated locations for NP_001005609.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The resulting isoform (2, also known as EDA-A2) has the same N- and C-termini but is shorter than isoform 1.
    Source sequence(s)
    AF040628, AL158141, BC144051, BQ008767
    Consensus CDS
    CCDS43966.1
    UniProtKB/TrEMBL
    A0A0K0KSD3, A0A0U5J797
    Related
    ENSP00000363681.2, ENST00000374553.6
    Conserved Domains (1) summary
    cd00184
    Location:249 → 381
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

  2. NM_001005610.4 → NP_001005610.2  ectodysplasin-A isoform 3

    See identical proteins and their annotated locations for NP_001005610.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (3, also known as EDA-O) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC144049, CA433299, FO393403, U59228
    Consensus CDS
    CCDS35318.2
    UniProtKB/Swiss-Prot
    Q92838
    Related
    ENSP00000434195.1, ENST00000525810.5

  3. NM_001005612.3 → NP_001005612.2  ectodysplasin-A isoform 5

    See identical proteins and their annotated locations for NP_001005612.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses two alternate in-frame splice sites compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter than isoform 1.
    Source sequence(s)
    AF061189, AL158141, BC144049, BU608133
    Consensus CDS
    CCDS35319.2
    UniProtKB/TrEMBL
    A0A0K0KSD3
    Related
    ENSP00000432585.1, ENST00000524573.5
    Conserved Domains (1) summary
    cd00184
    Location:249 → 378
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

  4. NM_001005613.4 → NP_001005613.1  ectodysplasin-A isoform 6

    See identical proteins and their annotated locations for NP_001005613.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (6, also known as EDA-E) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF061193, BC144049, CA433299, FO393403
    Consensus CDS
    CCDS55436.1
    UniProtKB/Swiss-Prot
    Q92838
    Related
    ENSP00000434861.1, ENST00000527388.5

  5. NM_001399.5 → NP_001390.1  ectodysplasin-A isoform 1

    See identical proteins and their annotated locations for NP_001390.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as EDA-A1).
    Source sequence(s)
    AF040628, AL158141, BC126143, BQ008767
    Consensus CDS
    CCDS14394.1
    UniProtKB/Swiss-Prot
    A0AUZ2, A2A337, B7ZLU2, B7ZLU4, O75910, Q5JS00, Q5JUM7, Q92838, Q9UP77, Q9Y6L0, Q9Y6L1, Q9Y6L2, Q9Y6L3, Q9Y6L4
    UniProtKB/TrEMBL
    A0A0K0KSD3
    Related
    ENSP00000363680.4, ENST00000374552.9
    Conserved Domains (1) summary
    cl00147
    Location:249 → 383
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    69616113..70039472
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029336.2 → XP_016884825.1  ectodysplasin-A isoform X2

    UniProtKB/TrEMBL
    A0A0K0KSD3
    Conserved Domains (1) summary
    cl00147
    Location:249 → 369
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

  2. XM_006724630.3 → XP_006724693.1  ectodysplasin-A isoform X1

    See identical proteins and their annotated locations for XP_006724693.1

    UniProtKB/TrEMBL
    A0A0K0KSD3
    Conserved Domains (1) summary
    cd00184
    Location:249 → 380
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

  3. XM_011530885.3 → XP_011529187.1  ectodysplasin-A isoform X3

    Conserved Domains (1) summary
    cl00147
    Location:249 → 325
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

  4. XM_017029337.2 → XP_016884826.1  ectodysplasin-A isoform X4

RNA

  1. XR_001755660.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    68049526..68472825
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326644.1 → XP_054182619.1  ectodysplasin-A isoform X2

  2. XM_054326643.1 → XP_054182618.1  ectodysplasin-A isoform X1

  3. XM_054326645.1 → XP_054182620.1  ectodysplasin-A isoform X3

  4. XM_054326646.1 → XP_054182621.1  ectodysplasin-A isoform X4

RNA

  1. XR_008485459.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001005611.1: Suppressed sequence

    Description
    NM_001005611.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NM_001005614.1: Suppressed sequence

    Description
    NM_001005614.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92838.2 GenPept UniProtKB/Swiss-Prot:Q92838

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