EPHB6

EPH receptor B6, the group of EPH receptors|Sterile alpha motif domain containing

Basic information

Region (hg38): 7:142855061-142871094

Links

ENSG00000106123

∙ NCBI:2051 ∙ OMIM:602757 ∙ HGNC:3396 ∙ Uniprot:O15197 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPHB6 gene.

not_specified (123 variants)
not_provided (2 variants)
Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHB6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004445.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			118 clinvar	7 clinvar		125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	118	7	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHB6	protein_coding	protein_coding	ENST00000392957	16	16056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-7	1.00	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.981	535	603	0.888	0.0000413	6520
Missense in Polyphen		207	256.76	0.80619		2816
Synonymous	-0.912	268	250	1.07	0.0000162	2207
Loss of Function	3.66	20	47.1	0.424	0.00000272	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000472	0.000470
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000165	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000165	0.000163
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Kinase-defective receptor for members of the ephrin-B family. Binds to ephrin-B1 and ephrin-B2. Modulates cell adhesion and migration by exerting both positive and negative effects upon stimulation with ephrin-B2. Inhibits JNK activation, T-cell receptor-induced IL-2 secretion and CD25 expression upon stimulation with ephrin-B2. {ECO:0000269|PubMed:12517763, ECO:0000269|PubMed:15955811}.;
Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;Axon guidance (Consensus)

Recessive Scores

pRec: 0.230

Intolerance Scores

loftool: 0.241
rvis_EVS: -1.43
rvis_percentile_EVS: 4

Haploinsufficiency Scores

pHI: 0.367
hipred: Y
hipred_score: 0.510
ghis: 0.541

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.721

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ephb6
Phenotype: cellular phenotype; normal phenotype; reproductive system phenotype; hematopoietic system phenotype; immune system phenotype;

Gene ontology

Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;peptidyl-tyrosine phosphorylation;ephrin receptor signaling pathway
Cellular component: extracellular region;cytosol;plasma membrane;integral component of plasma membrane;neuron projection;receptor complex
Molecular function: protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;ephrin receptor activity;transmembrane-ephrin receptor activity;ATP binding;signaling receptor activity