EMC6

protein-coding

ER membrane protein complex subunit 6, the group of ER membrane protein complex subunits

Gene summary

Contributes to membrane insertase activity. Involved in autophagosome assembly; protein insertion into ER membrane by stop-transfer membrane-anchor sequence; and tail-anchored membrane protein insertion into ER membrane. Located in endoplasmic reticulum membrane and omegasome membrane. Part of EMC complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TMEM93

MANE transcript

NM_031298.4

Inheritance

—

ClinVar variants

U:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:3,668,812-3,669,668

External References & Databases

Ensembl (ENSG00000127774)

Transcript & Mutation Effects

hg38 • Region Span ~0.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EMC6 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031298.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	12	0	0	12

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031298.4	RefSeq	NP_112588.1	1	MANE Select
ENST00000248378.6	Ensembl	ENSP00000248378.4	1	MANE Select
NM_001014764.3	RefSeq	NP_001014764.1	1	Standard
ENST00000397133.2	Ensembl	ENSP00000380322.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

autophagosome assembly
protein folding in endoplasmic reticulum

Molecular Function

protein binding

Cellular Component

integral component of membrane
integral component of endoplasmic reticulum membrane
ER membrane protein complex
integral component of omegasome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397133
Coding exons: 1
Length: 854
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125722
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.15	38	63.8	0.595	0.00000286	677
Missense (PolyPhen)		9	25.098	0.3586		271
Synonymous	-1.95	48	33.6	1.43	0.00000156	262
Loss of Function	1.36	0	2.14	0.00	9.02e-8	28

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.124

Intolerance Scores

RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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