EMCN

protein-coding

endomucin, the group of Mucins

Gene summary

EMCN is a mucin-like sialoglycoprotein that interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix (Kinoshita et al., 2001 [PubMed 11418125]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_016242.4

Inheritance

—

ClinVar variants

U:38B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr4:100,395,341-100,880,126

External References & Databases

Ensembl (ENSG00000164035)

Transcript & Mutation Effects

hg38 • Region Span ~484.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EMCN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016242.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			37 clinvar	3 clinvar	1 clinvar	41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	38	3	2	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016242.4	RefSeq	NP_057326.2	11	MANE Select
ENST00000296420.9	Ensembl	ENSP00000296420.4	11	MANE Select
NM_001159694.2	RefSeq	NP_001153166.1	10	Standard
ENST00000305864.7	Ensembl	ENSP00000304780.3	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296420
Coding exons: 11
Length: 484786
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 68
Defined: 125741
p: 0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.551	147	129	1.14	0.00000608	1661
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.0017	0.0017	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.468

Gene Damage Prediction

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