MIX23

protein-coding

mitochondrial matrix import factor 23

Gene summary

Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CCDC58

MANE transcript

NM_001017928.4

Inheritance

—

ClinVar variants

U:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr3:122,359,591-122,383,231

External References & Databases

Ensembl (ENSG00000160124)

Transcript & Mutation Effects

hg38 • Region Span ~23.6 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 MIX23 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001017928.4. 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			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	17	0	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001017928.4	RefSeq	NP_001017928.1	5	MANE Select
ENST00000291458.9	Ensembl	ENSP00000291458.5	5	MANE Select
NM_001308326.2	RefSeq	NP_001295255.1	5	Standard
ENST00000479414.1	Ensembl	ENSP00000418810.1	5	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000291458
Coding exons: 5
Length: 23641
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125733
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.896	53	74.8	0.708	0.00000360	949
Missense (PolyPhen)		10	16.665	0.60007		232
Synonymous	-0.544	31	27.4	1.13	0.00000150	245
Loss of Function	1.29	5	9.24	0.541	4.75e-7	110

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000092	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.623
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.508

Gene Damage Prediction

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