MTX3

protein-coding

metaxin 3, 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]

MANE transcript

NM_001363818.2

Inheritance

—

ClinVar variants

U:43B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr5:79,976,716-79,991,262

External References & Databases

Ensembl (ENSG00000177034)

Transcript & Mutation Effects

hg38 • Region Span ~14.5 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 MTX3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363818.2. 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	1 clinvar		2
missense			42 clinvar			42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	1	0	44

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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_001363818.2	RefSeq	NP_001350747.1	9	MANE Select
ENST00000512528.3	Ensembl	ENSP00000424798.2	9	MANE Select
NM_001010891.5	RefSeq	NP_001010891.4	8	Standard
NM_001167741.2	RefSeq	NP_001161213.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport

Cellular Component

mitochondrial sorting and assembly machinery complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000512560
Coding exons: 7
Length: 11499
Individuals with no LoFs: 124610
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 124635
p: 0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.124	118	122	0.968	0.00000617	1618
Missense (PolyPhen)		40	49.693	0.80494		695
Synonymous	0.325	42	44.8	0.938	0.00000215	493
Loss of Function	1.46	8	13.8	0.578	7.50e-7	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00032	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Could function in transport of proteins into the mitochondrion. {ECO:0000250}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.877
RVIS EVS: 0.51
RVIS percentile EVS: 80.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00903

Gene Damage Prediction

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