EDA2R

ectodysplasin A2 receptor, the group of Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): X:66595637-66639298

Links

ENSG00000131080 ∙ NCBI:60401 ∙ OMIM:300276 ∙ HGNC:17756 ∙ Uniprot:Q9HAV5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked hypohidrotic ectodermal dysplasia (Supportive), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EDA2R gene.

• not_specified (28 variants)
• not_provided (9 variants)
• Hypohidrotic_X-linked_ectodermal_dysplasia (1 variants)
• Hypodontia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDA2R gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021783.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense			21	7	1	29
nonsense						0
start loss						0
frameshift		1	1			2
splice donor/acceptor (+/-2bp)						0
Total	0	1	22	11	3

Highest pathogenic variant AF is 0.000005471597

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDA2R	protein_coding	protein_coding	ENST00000450752	6	43630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000547	0.718	125542	14	16	125572	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.205	114	108	1.06	0.00000813	2061
Missense in Polyphen		33	28.791	1.1462		625
Synonymous	-1.91	57	41.4	1.38	0.00000317	602
Loss of Function	0.877	6	8.81	0.681	6.29e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000541	0.000448
Ashkenazi Jewish	0.00	0.00
East Asian	0.000147	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000138	0.0000969
Middle Eastern	0.000147	0.000109
South Asian	0.000487	0.000261
Other	0.000227	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for EDA isoform A2, but not for EDA isoform A1. Mediates the activation of the NF-kappa-B and JNK pathways. Activation seems to be mediated by binding to TRAF3 and TRAF6. {ECO:0000269|PubMed:12270937}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Ectoderm Differentiation;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.386
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0197
• hipred: N
• hipred_score: 0.327
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0615

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Eda2r
• Phenotype: normal phenotype

Gene ontology

• Biological process: multicellular organism development;epidermis development;ectodermal cell differentiation;tumor necrosis factor-mediated signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of JNK cascade;positive regulation of NF-kappaB transcription factor activity;intrinsic apoptotic signaling pathway by p53 class mediator
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: tumor necrosis factor-activated receptor activity;protein binding;signaling receptor activity