EMCN

endomucin, the group of Mucins

Basic information

Region (hg38): 4:100395340-100880126

Links

ENSG00000164035 ∙ NCBI:51705 ∙ OMIM:608350 ∙ HGNC:16041 ∙ Uniprot:Q9ULC0 ∙ 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 EMCN gene.

• Inborn genetic diseases (14 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMCN 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			13	1	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	2

Variants in EMCN

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

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

Position	Type	Phenotype	Significance	ClinVar
4-100410350-G-A		not specified	Uncertain significance (Aug 28, 2023)
4-100415922-C-T		not specified	Uncertain significance (Mar 29, 2022)
4-100415923-G-A			Benign (Nov 14, 2017)
4-100415933-T-C		not specified	Uncertain significance (Dec 27, 2022)
4-100415958-G-T		not specified	Uncertain significance (Feb 06, 2023)
4-100421321-G-C		not specified	Uncertain significance (Jul 06, 2021)
4-100421360-C-A		not specified	Uncertain significance (Mar 02, 2023)
4-100423363-T-A		not specified	Uncertain significance (Jan 05, 2022)
4-100447571-G-T		not specified	Uncertain significance (May 23, 2023)
4-100465440-T-C		not specified	Uncertain significance (May 24, 2023)
4-100465486-C-T			Benign (Apr 03, 2018)
4-100465504-C-T		not specified	Uncertain significance (Oct 12, 2021)
4-100475053-T-C		not specified	Uncertain significance (Jun 01, 2023)
4-100479931-C-G		not specified	Uncertain significance (Jan 10, 2023)
4-100479986-T-C		not specified	Likely benign (Jul 14, 2021)
4-100517854-T-C		not specified	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMCN	protein_coding	protein_coding	ENST00000296420	11	484786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000864	0.937	125673	0	68	125741	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.551	147	129	1.14	0.00000608	1661
Missense in Polyphen		87	70.203	1.2393		926
Synonymous	0.0225	43	43.2	0.996	0.00000208	531
Loss of Function	1.69	9	16.4	0.549	7.79e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000870	0.0000870
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.00171	0.00170
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endothelial sialomucin, also called endomucin or mucin- like sialoglycoprotein, which interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix.

Intolerance Scores

• loftool: 0.225
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.312
• hipred: N
• hipred_score: 0.123
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emcn

Gene ontology

• Cellular component: extracellular region;plasma membrane;integral component of membrane