EDA2R

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

Basic information

Region (hg38): X:66595636-66639298

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.

• Inborn genetic diseases (12 variants)
• not provided (11 variants)
• not specified (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	2	5
missense			8	5	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	8	9	4

Variants in EDA2R

This is a list of pathogenic ClinVar variants found in the EDA2R region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-66598007-T-A			Likely benign (Feb 01, 2023)
X-66599554-C-T		not specified	Uncertain significance (Sep 14, 2022)
X-66599555-C-A		not specified	Conflicting classifications of pathogenicity (Jun 01, 2022)
X-66599555-C-G		not specified	Likely benign (Sep 21, 2023)
X-66599555-C-T		not specified	Likely benign (Jan 10, 2023)
X-66599650-C-T		not specified	Uncertain significance (Oct 27, 2023)
X-66599652-C-T			Benign (Sep 19, 2018)
X-66599665-G-T		not specified	Uncertain significance (Feb 17, 2022)
X-66599693-G-A		not specified	Uncertain significance (Feb 17, 2024)
X-66599718-G-A			Likely benign (Jan 24, 2018)
X-66599738-G-A		not specified	Uncertain significance (Jun 09, 2022)
X-66599773-G-A		not specified	Uncertain significance (Nov 08, 2021)
X-66599776-T-C		not specified	Uncertain significance (Sep 21, 2023)
X-66599804-C-T		not specified	Likely benign (Jan 10, 2023)
X-66602672-G-A		not specified	Uncertain significance (Mar 06, 2023)
X-66602765-T-T			Benign (Oct 24, 2018)
X-66602772-C-T			Likely benign (Dec 31, 2019)
X-66604439-G-A		not specified	Likely benign (Dec 14, 2018)
X-66604444-T-G			Uncertain significance (Oct 13, 2017)
X-66604490-G-A		not specified	Uncertain significance (Jan 04, 2022)
X-66604498-C-T		not specified	Likely benign (Jan 26, 2022)
X-66605060-TC-T		Hypohidrotic X-linked ectodermal dysplasia	Uncertain significance (Aug 01, 2012)
X-66605082-T-G		not specified	Uncertain significance (Aug 21, 2023)
X-66605179-A-T			Likely benign (Sep 13, 2017)
X-66605180-G-A		not specified	Uncertain significance (Oct 13, 2023)

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