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.

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.

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						0
missense			59	5		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	60	5	0

Variants in EPHB6

This is a list of pathogenic ClinVar variants found in the EPHB6 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-142863324-G-C		not specified	Uncertain significance (Sep 30, 2024)
7-142863997-G-C		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
7-142864093-G-A		not specified	Uncertain significance (Jan 29, 2024)
7-142864111-A-G		not specified	Uncertain significance (Oct 03, 2022)
7-142864149-C-G		not specified	Uncertain significance (Oct 09, 2024)
7-142864198-G-A		not specified	Uncertain significance (Jun 16, 2024)
7-142864219-G-C		not specified	Uncertain significance (Nov 01, 2022)
7-142864231-T-C		not specified	Uncertain significance (Nov 07, 2024)
7-142864246-T-G		not specified	Uncertain significance (Aug 04, 2024)
7-142864252-G-T		not specified	Uncertain significance (May 24, 2023)
7-142864294-C-T		not specified	Uncertain significance (Oct 12, 2021)
7-142864308-T-G		not specified	Uncertain significance (Jun 05, 2024)
7-142864350-C-G		not specified	Uncertain significance (Mar 20, 2024)
7-142864355-C-A		not specified	Uncertain significance (Sep 01, 2021)
7-142864389-G-C		not specified	Uncertain significance (Nov 23, 2022)
7-142864537-C-A		not specified	Uncertain significance (Jul 09, 2021)
7-142864537-C-T		not specified	Uncertain significance (Apr 10, 2023)
7-142864554-G-T		not specified	Uncertain significance (May 29, 2024)
7-142864627-G-A		not specified	Uncertain significance (Apr 09, 2024)
7-142864665-G-A		not specified	Uncertain significance (Jan 18, 2023)
7-142864692-G-A		not specified	Uncertain significance (Nov 03, 2023)
7-142864702-G-A		not specified	Uncertain significance (Oct 12, 2021)
7-142865486-G-T		not specified	Uncertain significance (Aug 08, 2022)
7-142865545-C-G		not specified	Uncertain significance (Nov 24, 2024)
7-142865546-G-A		not specified	Uncertain significance (Mar 25, 2024)

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
• 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