EMC2

ER membrane protein complex subunit 2, the group of ER membrane protein complex subunits|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 8:108443601-108489196

Previous symbols: [ "KIAA0103", "TTC35" ]

Links

ENSG00000104412 ∙ NCBI:9694 ∙ OMIM:607722 ∙ HGNC:28963 ∙ Uniprot:Q15006 ∙ 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 EMC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMC2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in EMC2

This is a list of pathogenic ClinVar variants found in the EMC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-108449912-T-C		not specified	Uncertain significance (Sep 02, 2024)
8-108450491-T-C		not specified	Uncertain significance (Jan 21, 2025)
8-108455886-A-C		not specified	Uncertain significance (Jul 30, 2024)
8-108455895-T-C		not specified	Uncertain significance (Apr 09, 2024)
8-108455928-A-C		not specified	Uncertain significance (Jun 18, 2024)
8-108469850-A-G		not specified	Uncertain significance (Oct 22, 2024)
8-108469862-C-G		not specified	Uncertain significance (Oct 26, 2021)
8-108470112-A-G		not specified	Uncertain significance (May 28, 2024)
8-108475928-C-T		not specified	Uncertain significance (Nov 25, 2024)
8-108476792-C-G		not specified	Uncertain significance (Jul 12, 2023)
8-108476812-C-G		not specified	Uncertain significance (Aug 05, 2023)
8-108486560-G-A		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMC2	protein_coding	protein_coding	ENST00000220853	11	43316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00330	0.995	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.620	128	149	0.857	0.00000725	1957
Missense in Polyphen		20	34.633	0.57748		476
Synonymous	-0.407	52	48.4	1.07	0.00000223	493
Loss of Function	2.71	8	21.6	0.371	0.00000106	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000112	0.000109
South Asian	0.00	0.00
Other	0.000343	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.308
• hipred: N
• hipred_score: 0.322
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Emc2

Gene ontology

• Biological process: protein folding in endoplasmic reticulum
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum;ER membrane protein complex
• Molecular function: protein binding