EMP3

protein-coding

epithelial membrane protein 3

Gene summary

The protein encoded by this gene belongs to the PMP-22/EMP/MP20 family of proteins. The protein contains four transmembrane domains and two N-linked glycosylation sites. It is thought to be involved in cell proliferation, cell-cell interactions and function as a tumor suppressor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

MANE transcript

NM_001425.3

Inheritance

—

ClinVar variants

U:28

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr19:48,321,310-48,330,559

External References & Databases

Ensembl (ENSG00000142227)

Transcript & Mutation Effects

hg38 • Region Span ~9.2 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 EMP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 25

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001425.3. 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						0
missense			26 clinvar			26
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	28	0	0	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001425.3	RefSeq	NP_001416.1	4	MANE Select
ENST00000270221.11	Ensembl	ENSP00000270221.5	4	MANE Select
NM_001313905.1	RefSeq	NP_001300834.1	4	Standard
ENST00000593437.1	Ensembl	ENSP00000469275.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell death
negative regulation of cell population proliferation
bleb assembly

Molecular Function

protein binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000270221
Coding exons: 4
Length: 9045
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 69
Defined: 125747
p: 0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.626	81	98.5	0.822	0.00000557	1045
Missense (PolyPhen)		28	38.177	0.73342		429
Synonymous	0.687	38	43.8	0.868	0.00000291	334
Loss of Function	0.276	9	9.94	0.905	6.08e-7	89

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.0025	0.0025	notable
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.00016	0.00016	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably involved in cell proliferation and cell-cell interactions.;

Recessive Scores

pRec: 0.154

Intolerance Scores

LoFtool: 0.544
RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.473

Gene Damage Prediction

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