MTX1

protein-coding

metaxin 1, the group of Metaxins

Gene summary

Predicted to be involved in mitochondrial outer membrane translocase complex assembly and protein insertion into mitochondrial outer membrane. Located in mitochondrion. Part of MIB complex and SAM complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MANE transcript

NM_002455.5

Inheritance

—

ClinVar variants

U:41

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr1:155,208,695-155,213,824

External References & Databases

Ensembl (ENSG00000173171)

Transcript & Mutation Effects

hg38 • Region Span ~5.1 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 MTX1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 38

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002455.5. 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			1
missense			36 clinvar			36
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	41	0	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002455.5	RefSeq	NP_002446.3	8	MANE Select
ENST00000368376.8	Ensembl	ENSP00000357360.3	8	MANE Select
NM_198883.3	RefSeq	NP_942584.2	7	Standard
ENST00000316721.8	Ensembl	ENSP00000317106.4	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
Metabolism of proteins
Mitochondrial protein import

Biological Process

lactation
protein transport

Cellular Component

mitochondrial sorting and assembly machinery complex
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368376
Coding exons: 8
Length: 5126
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125747
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.190	197	190	1.04	0.0000101	2898
Missense (PolyPhen)		64	63.963	1.0006		1039
Synonymous	-0.902	86	76.0	1.13	0.00000372	1018
Loss of Function	2.40	6	16.5	0.364	9.26e-7	221

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in transport of proteins into the mitochondrion. Essential for embryonic development (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0982

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.603

Gene Damage Prediction

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