MPEG1

protein-coding

macrophage expressed 1

Gene summary

Enables wide pore channel activity. Involved in defense response to Gram-negative bacterium and defense response to Gram-positive bacterium. Located in cytoplasmic vesicle. Is active in phagolysosome membrane. Implicated in primary immunodeficiency disease. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001039396.2

Inheritance

ClinVar variants

P:2U:128B:26

Top phenotype

Immunodeficiency 77

gnomAD constraint

pLI —, LoF o/e 1.15

Max pathogenic AF

—

Genomic locus

chr11:59,208,510-59,212,927

External References & Databases

Ensembl (ENSG00000197629)

Transcript & Mutation Effects

hg38 • Region Span ~4.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immunodeficiency 77LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030973

Submitter: Labcorp Genetics (formerly Invitae)

immunodeficiency 77STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030973

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Immunodeficiency 77AD

Manifestation: Allergy/Immunology/Infectious

Intervention: Allergy/Immunology/Infectious

Rationale: Individuals have been described with recurrent and severe polymicrobial infections, including involving with unusual organisms, and awareness may allow preventative measures and early and aggressive management of infections and related sequelae (eg, treatment with gamma-IFN has been suggested to be as a potentially effective therapeutic modality)

Refs: 28422754; 33224153

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MPEG1 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 120

Immunodeficiency 77Total: 20

not providedTotal: 19

MPEG1-related disorderTotal: 4

Primary ciliary dyskinesia 3Total: 1

MPEG1-related immunodeficiencyTotal: 1

Castleman-Kojima diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039396.2. 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			1 clinvar	9 clinvar	3 clinvar	13
missense	1 clinvar		120 clinvar	14 clinvar		135
nonsense	1 clinvar		4 clinvar			5
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)						0
Total	2	0	128	23	3	156

Highest pathogenic variant AF is 0.000032836408

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039396.2	RefSeq	NP_001034485.1	1	MANE Select
ENST00000361050.4	Ensembl	ENSP00000354335.3	1	MANE Select
ENST00000877842.1	Ensembl	ENSP00000547901.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell Cycle

Biological Process

defense response to bacterium

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361050
Coding exons: 1
Length: 4442
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0528	390	387	1.01	0.0000214	4677
Missense (PolyPhen)		97	112.18	0.8647		1433
Synonymous	-2.21	199	163	1.22	0.00000986	1481
Loss of Function	-0.611	22	19.1	1.15	0.00000117	208

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.435
RVIS EVS: 0.16
RVIS percentile EVS: 64.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.330

Gene Damage Prediction

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