SLC25A23

protein-coding

solute carrier family 25 member 23, the group of Solute carrier family 25|EF-hand domain containing

Gene summary

Enables ADP:phosphate antiporter activity and ATP:phosphate antiporter activity. Involved in several processes, including calcium import into the mitochondrion; mitochondrial ATP transmembrane transport; and positive regulation of mitochondrial calcium ion concentration. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024103.3

Inheritance

—

ClinVar variants

U:97B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr19:6,436,079-6,465,203

External References & Databases

Ensembl (ENSG00000125648)

Transcript & Mutation Effects

hg38 • Region Span ~29.1 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 SLC25A23 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024103.3. 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			2 clinvar	2 clinvar	3 clinvar	7
missense			93 clinvar	1 clinvar		94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	97	3	3	103

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 82 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024103.3	RefSeq	NP_077008.2	10	MANE Select
ENST00000301454.9	Ensembl	ENSP00000301454.3	10	MANE Select
ENST00000264088.8	Ensembl	ENSP00000264088.3	11	Standard
ENST00000334510.9	Ensembl	ENSP00000334537.4	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of oxidative phosphorylation
mitochondrial calcium ion transmembrane transport
ATP transport
calcium import into the mitochondrion
regulation of cellular respiration

Molecular Function

ATP transmembrane transporter activity
calcium ion binding
protein binding

Cellular Component

mitochondrion
mitochondrial inner membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301454
Coding exons: 10
Length: 29125
Individuals with no LoFs: 125576
Homozygous LoFs: 1
Heterozygous LoFs: 171
Defined: 125748
p: 0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.70	221	305	0.726	0.0000195	2995
Missense (PolyPhen)		95	136.78	0.69457		1292
Synonymous	0.193	120	123	0.978	0.00000772	961
Loss of Function	2.93	9	24.7	0.364	0.00000130	241

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.0074	0.0070	notable
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000065	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-dependent mitochondrial solute carrier. Mitochondrial solute carriers shuttle metabolites, nucleotides, and cofactors through the mitochondrial inner membrane (PubMed:15123600). May act as a ATP-Mg/Pi exchanger that mediates the transport of Mg-ATP in exchange for phosphate, catalyzing the net uptake or efflux of adenine nucleotides into or from the mitochondria (PubMed:15123600). Acts as a regulator of mitochondrial calcium uptake via interaction with MCU and MICU1 (PubMed:24430870). {ECO:0000269|PubMed:15123600, ECO:0000269|PubMed:24430870}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.257
RVIS EVS: -1.02
RVIS percentile EVS: 8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.197

Gene Damage Prediction

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