EMC9

ER membrane protein complex subunit 9, the group of ER membrane protein complex subunits

Basic information

Region (hg38): 14:24138959-24141591

Previous symbols: [ "C14orf122", "FAM158A" ]

Links

ENSG00000100908 ∙ NCBI:51016 ∙ ∙ HGNC:20273 ∙ Uniprot:Q9Y3B6 ∙ 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 EMC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMC9 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in EMC9

This is a list of pathogenic ClinVar variants found in the EMC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24139102-G-T		not specified	Uncertain significance (Nov 02, 2023)
14-24139122-A-C		not specified	Uncertain significance (Aug 08, 2022)
14-24139129-G-C		not specified	Uncertain significance (Dec 20, 2023)
14-24139132-G-A		not specified	Uncertain significance (Jul 25, 2023)
14-24139138-G-C		not specified	Uncertain significance (Feb 17, 2024)
14-24139172-C-G		not specified	Uncertain significance (Feb 22, 2023)
14-24139191-A-G		not specified	Uncertain significance (Jul 05, 2022)
14-24139384-C-A		not specified	Uncertain significance (Apr 06, 2022)
14-24139424-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-24139591-A-G		not specified	Uncertain significance (Oct 05, 2022)
14-24140955-C-G		not specified	Uncertain significance (Dec 21, 2022)
14-24140956-A-G		not specified	Uncertain significance (Feb 01, 2023)
14-24140962-C-A		not specified	Uncertain significance (Aug 19, 2021)
14-24141153-T-G		not specified	Uncertain significance (Mar 20, 2023)
14-24141187-A-C		not specified	Uncertain significance (Dec 19, 2023)
14-24141190-C-T		not specified	Uncertain significance (Jan 18, 2022)
14-24141193-C-G		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMC9	protein_coding	protein_coding	ENST00000419198	5	2624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00132	0.871	125625	2	121	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.221	115	122	0.944	0.00000668	1345
Missense in Polyphen		38	43.451	0.87454		527
Synonymous	1.28	36	47.2	0.762	0.00000235	428
Loss of Function	1.32	6	10.6	0.563	5.41e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.0000544	0.0000544
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000422	0.000422
Middle Eastern	0.0000544	0.0000544
South Asian	0.00173	0.00167
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0954

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.248
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emc9

Gene ontology

• Cellular component: cytoplasm;ER membrane protein complex
• Molecular function: protein binding