EMB

embigin, the group of Basigin family |I-set domain containing

Basic information

Region (hg38): 5:50396192-50443248

Links

ENSG00000170571 ∙ NCBI:133418 ∙ OMIM:615669 ∙ HGNC:30465 ∙ Uniprot:Q6PCB8 ∙ 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 EMB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMB 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				1		1
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in EMB

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

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

Position	Type	Phenotype	Significance	ClinVar
5-50399862-T-A		not specified	Uncertain significance (Dec 01, 2022)
5-50402294-A-C		not specified	Uncertain significance (Jan 16, 2025)
5-50403188-C-G		not specified	Uncertain significance (Jun 21, 2021)
5-50403285-T-C		not specified	Uncertain significance (May 29, 2024)
5-50403294-A-T		not specified	Uncertain significance (Feb 27, 2024)
5-50403332-G-T		not specified	Uncertain significance (May 16, 2023)
5-50403375-A-G		not specified	Uncertain significance (Feb 21, 2024)
5-50403387-T-G		not specified	Uncertain significance (Nov 13, 2024)
5-50405787-A-G		not specified	Uncertain significance (Jan 19, 2024)
5-50410915-C-T		not specified	Likely benign (Aug 07, 2024)
5-50411242-T-C		not specified	Uncertain significance (Jun 01, 2023)
5-50411254-T-C		not specified	Uncertain significance (Feb 13, 2023)
5-50411260-C-G		not specified	Uncertain significance (Jan 15, 2025)
5-50411333-T-C		not specified	Uncertain significance (May 26, 2023)
5-50411354-T-C		not specified	Uncertain significance (Jan 09, 2024)
5-50411355-A-T		not specified	Uncertain significance (Dec 21, 2023)
5-50411365-A-G		not specified	Uncertain significance (Oct 01, 2024)
5-50441081-A-G		not specified	Uncertain significance (Dec 06, 2022)
5-50441095-G-A			Likely benign (Jan 11, 2018)
5-50441119-C-G		not specified	Uncertain significance (Sep 09, 2024)
5-50441124-C-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMB	protein_coding	protein_coding	ENST00000303221	9	47057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-11	0.0445	125664	0	43	125707	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.556	174	155	1.13	0.00000709	2141
Missense in Polyphen		36	36.821	0.9777		551
Synonymous	-0.834	66	57.9	1.14	0.00000289	600
Loss of Function	0.0295	17	17.1	0.992	7.84e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000684	0.000674
Ashkenazi Jewish	0.00	0.00
East Asian	0.000174	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.000174	0.000163
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the outgrowth of motoneurons and in the formation of neuromuscular junctions. Following muscle denervation, promotes nerve terminal sprouting and the formation of additional acetylcholine receptor clusters at synaptic sites without affecting terminal Schwann cell number or morphology. Delays the retraction of terminal sprouts following re-innervation of denervated endplates. May play a role in targeting the monocarboxylate transporters SLC16A1 and SLC16A7 to the cell membrane (By similarity). {ECO:0000250}.
• Pathway: Bile salt and organic anion SLC transporters;Proton-coupled monocarboxylate transport;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.721
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.0359
• hipred: N
• hipred_score: 0.153
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emb
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;axon guidance;plasma membrane lactate transport;dendrite self-avoidance
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;axon;synapse
• Molecular function: monocarboxylic acid transmembrane transporter activity;cell-cell adhesion mediator activity