EMC3

ER membrane protein complex subunit 3, the group of ER membrane protein complex subunits

Basic information

Region (hg38): 3:9962682-10011202

Previous symbols: [ "TMEM111" ]

Links

ENSG00000125037 ∙ NCBI:55831 ∙ OMIM:620273 ∙ HGNC:23999 ∙ Uniprot:Q9P0I2 ∙ 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 EMC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMC3 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in EMC3

This is a list of pathogenic ClinVar variants found in the EMC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9964111-G-A			Likely benign (May 01, 2022)
3-9969742-C-T		not specified	Uncertain significance (Dec 17, 2023)
3-9969753-A-G		not specified	Uncertain significance (May 07, 2024)
3-9970618-G-A		not specified	Uncertain significance (Sep 30, 2022)
3-9970632-T-C		not specified	Uncertain significance (Apr 01, 2024)
3-9977432-C-T		not specified	Uncertain significance (May 17, 2023)
3-9986533-C-G		not specified	Uncertain significance (Mar 29, 2022)
3-9986541-C-G		not specified	Uncertain significance (Dec 03, 2021)
3-9986541-C-T		not specified	Uncertain significance (Jun 05, 2024)
3-9986547-G-C		not specified	Uncertain significance (Sep 16, 2021)
3-9986634-A-C		not specified	Uncertain significance (Jun 26, 2024)
3-10007364-G-C		not specified	Uncertain significance (Aug 10, 2021)
3-10007622-C-T		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMC3	protein_coding	protein_coding	ENST00000245046	8	48580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.286	0.714	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	83	149	0.556	0.00000763	1732
Missense in Polyphen		9	44.835	0.20073		556
Synonymous	-0.317	56	53.1	1.06	0.00000276	480
Loss of Function	2.89	4	16.7	0.239	9.48e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000951	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000460	0.0000440
Middle Eastern	0.000113	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0790

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.728
• ghis: 0.421

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emc3

Zebrafish Information Network

• Gene name: emc3
• Affected structure: retinal cone cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: biological_process;protein folding in endoplasmic reticulum
• Cellular component: integral component of membrane;ER membrane protein complex
• Molecular function: molecular_function