EMC4

ER membrane protein complex subunit 4, the group of ER membrane protein complex subunits

Basic information

Region (hg38): 15:34225012-34230156

Previous symbols: [ "TMEM85" ]

Links

ENSG00000128463 ∙ NCBI:51234 ∙ OMIM:616245 ∙ HGNC:28032 ∙ Uniprot:Q5J8M3 ∙ 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 EMC4 gene.

• Agenesis of the corpus callosum with peripheral neuropathy (4 variants)
• not provided (2 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMC4 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			2			2
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	7	1	0

Variants in EMC4

This is a list of pathogenic ClinVar variants found in the EMC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-34225122-C-T		not specified	Uncertain significance (Mar 22, 2023)
15-34227694-G-A		not specified	Uncertain significance (Oct 12, 2021)
15-34227813-C-T			Uncertain significance (Feb 16, 2016)
15-34230039-C-A		Agenesis of the corpus callosum with peripheral neuropathy	Uncertain significance (Jan 13, 2018)
15-34230053-A-C		Agenesis of the corpus callosum with peripheral neuropathy	Uncertain significance (Jan 12, 2018)
15-34230058-CAT-C			Likely benign (Nov 01, 2022)
15-34230072-CAA-C		Agenesis of the corpus callosum with peripheral neuropathy	Uncertain significance (Jun 14, 2016)
15-34230126-A-G		Agenesis of the corpus callosum with peripheral neuropathy	Uncertain significance (Jan 13, 2018)
15-34230149-T-TA		Agenesis of the corpus callosum with peripheral neuropathy	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMC4	protein_coding	protein_coding	ENST00000267750	5	5158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.861	0.139	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	68	105	0.648	0.00000517	1189
Missense in Polyphen		22	33.005	0.66657		372
Synonymous	-0.574	42	37.5	1.12	0.00000186	355
Loss of Function	2.77	1	10.8	0.0922	5.52e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May mediate anti-apoptotic activity.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.0350
• hipred: Y
• hipred_score: 0.594
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• 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: Emc4
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: apoptotic process;protein folding in endoplasmic reticulum
• Cellular component: integral component of membrane;ER membrane protein complex