EMC7

ER membrane protein complex subunit 7, the group of ER membrane protein complex subunits

Basic information

Region (hg38): 15:34084017-34101862

Previous symbols: [ "C15orf24" ]

Links

ENSG00000134153 ∙ NCBI:56851 ∙ ∙ HGNC:24301 ∙ Uniprot:Q9NPA0 ∙ 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 EMC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMC7 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in EMC7

This is a list of pathogenic ClinVar variants found in the EMC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-34084353-C-G		not specified	Uncertain significance (Aug 08, 2023)
15-34084386-G-A		not specified	Uncertain significance (May 20, 2024)
15-34084483-T-C		not specified	Uncertain significance (Jun 29, 2023)
15-34090429-G-A		not specified	Uncertain significance (Nov 07, 2022)
15-34095917-T-C		not specified	Uncertain significance (Apr 01, 2024)
15-34101611-A-C		not specified	Uncertain significance (Mar 18, 2024)
15-34101652-G-A		not specified	Uncertain significance (Oct 26, 2022)
15-34101713-C-G		not specified	Uncertain significance (Aug 11, 2022)
15-34101726-C-T			Benign (May 08, 2017)
15-34101749-C-T		not specified	Uncertain significance (Jun 05, 2023)
15-34101812-G-A		not specified	Likely benign (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMC7	protein_coding	protein_coding	ENST00000256545	5	17932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.867	0.133	125714	0	3	125717	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	90	136	0.664	0.00000637	1564
Missense in Polyphen		15	32.866	0.4564		407
Synonymous	0.525	48	52.9	0.908	0.00000266	501
Loss of Function	2.79	1	11.0	0.0911	5.33e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• pHI: 0.406
• hipred: Y
• hipred_score: 0.673
• ghis: 0.413

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• 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: Emc7
• Phenotype: homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane;ER membrane protein complex
• Molecular function: carbohydrate binding