EMP3

epithelial membrane protein 3

Basic information

Region (hg38): 19:48321310-48330559

Links

ENSG00000142227 ∙ NCBI:2014 ∙ OMIM:602335 ∙ HGNC:3335 ∙ Uniprot:P54852 ∙ 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 EMP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMP3 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			13			13
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	0	0

Variants in EMP3

This is a list of pathogenic ClinVar variants found in the EMP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48326866-G-A		not specified	Uncertain significance (Jun 29, 2022)
19-48326894-T-C		not specified	Uncertain significance (Apr 18, 2023)
19-48327540-G-A		not specified	Uncertain significance (Mar 07, 2025)
19-48327566-G-A		not specified	Uncertain significance (Sep 20, 2024)
19-48327584-G-A		not specified	Uncertain significance (Mar 07, 2025)
19-48327611-G-A		not specified	Uncertain significance (Jun 13, 2024)
19-48329378-A-T		not specified	Uncertain significance (Nov 21, 2022)
19-48329471-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-48329484-T-C		not specified	Uncertain significance (Aug 19, 2024)
19-48329490-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-48330337-T-C		not specified	Uncertain significance (Oct 06, 2021)
19-48330342-G-T		not specified	Uncertain significance (Sep 25, 2023)
19-48330435-G-C		not specified	Uncertain significance (Sep 08, 2024)
19-48330445-A-G		not specified	Uncertain significance (Jun 13, 2024)
19-48330463-G-A		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMP3	protein_coding	protein_coding	ENST00000270221	4	9045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000262	0.317	125678	0	69	125747	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.626	81	98.5	0.822	0.00000557	1045
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000484	0.000481
Ashkenazi Jewish	0.00248	0.00248
East Asian	0.000175	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000175	0.000163
South Asian	0.000164	0.000163
Other	0.000490	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.289
• hipred: N
• hipred_score: 0.335
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.473

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emp3

Gene ontology

• Biological process: cell death;negative regulation of cell population proliferation;bleb assembly
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding