EDA ectodysplasin A [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: Xq13.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (69616113..70039472)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (68049526..68472825)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (68835957..69259322)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Association between Circulating Ectodysplasin A and Diabetic Kidney Disease.
Title: Association between Circulating Ectodysplasin A and Diabetic Kidney Disease.
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.
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.
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.
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.
Two Novel Mutations in Ectodysplasin-A Identified in Syndromic Tooth Agenesis.
Title: Two Novel Mutations in Ectodysplasin-A Identified in Syndromic Tooth Agenesis.
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.
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.
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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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 EBI GWAS CatalogPubMed
Genome-wide association study reveals multiple loci associated with primary tooth development during infancy. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

DXS8269 (e-PCR)
- UniSTS:23053

DXS1325 (e-PCR)
- UniSTS:99603

DYS417 (e-PCR)
- UniSTS:9750

G06856 (e-PCR)
- UniSTS:53581

DXS1690 (e-PCR)
- UniSTS:148815

DXS8270 (e-PCR)
- UniSTS:82001

RH70680 (e-PCR)
- UniSTS:7507

DXS7625 (e-PCR)
- UniSTS:4713

DXS7773 (e-PCR)
- UniSTS:99703

RH41975 (e-PCR)
- UniSTS:24440

PMC24264P5 (e-PCR)
- UniSTS:272249

DXS106 (e-PCR)
- UniSTS:99215

DXS7845 (e-PCR)
- UniSTS:99482

WI-10638 (e-PCR)
- UniSTS:15526

DXS7791 (e-PCR)
- UniSTS:17321

RH47751 (e-PCR)
- UniSTS:4010

L78108 (e-PCR)
- UniSTS:39594

DXS1162 (e-PCR)
- UniSTS:150188

NoName (e-PCR)
- UniSTS:492214

DXS1422 (e-PCR)
- UniSTS:99554

NoName (e-PCR)
- UniSTS:482025

RH92962 (e-PCR)
- UniSTS:85749

L42647 (e-PCR)
- UniSTS:33023

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytokine activity	IDA Inferred from Direct Assay more info	PubMed
enables death receptor agonist activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables death receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables death receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables receptor ligand activity	IBA Inferred from Biological aspect of Ancestor more info
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 cytokine-mediated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cytokine-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
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 canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
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 regulation of non-canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
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

NG_009809.2 RefSeqGene

Range

5047..428406

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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
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 ...
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

69616113..70039472

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

RNA

XR_001755660.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

68049526..68472825

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0K0KSD3
XM_054326643.1 → XP_054182618.1 ectodysplasin-A isoform X1

UniProtKB/TrEMBL

A0A0K0KSD3
XM_054326645.1 → XP_054182620.1 ectodysplasin-A isoform X3
XM_054326646.1 → XP_054182621.1 ectodysplasin-A isoform X4

RNA

XR_008485459.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.
NM_001005614.1: Suppressed sequence

Description

NM_001005614.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.