SLC25A4

Chr 4ADAR

solute carrier family 25 member 4

Also known as: AAC1, ANT, ANT 1, ANT1, MTDPS12, MTDPS12A, PEO2, PEO3

The protein functions as a gated pore in the inner mitochondrial membrane that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm, forming a homodimer essential for cellular energy metabolism. Mutations cause mitochondrial DNA depletion syndrome with cardiomyopathy (both autosomal dominant and recessive forms) and autosomal dominant progressive external ophthalmoplegia with mitochondrial DNA deletions. The disease mechanism can vary by variant type, with some mutations likely acting through dominant-negative effects that disrupt the homodimer function.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
GOF/LOFmechanismAD/ARLOEUF 0.643 OMIM phenotypes
Clinical SummarySLC25A4
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Gene-Disease Validity (ClinGen)
Leigh syndrome · ADLimited

Limited evidence — not for standalone diagnostic reporting

2 total gene-disease associations curated

Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.20) despite low pLI — interpret in context.
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GeneReview available — SLC25A4
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.64LOEUF
pLI 0.453
Z-score 2.33
OE 0.20 (0.080.64)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.87Z-score
OE missense 0.60 (0.510.71)
105 obs / 174.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.20 (0.080.64)
00.351.4
Missense OE0.60 (0.510.71)
00.61.4
Synonymous OE1.02
01.21.6
LoF obs/exp: 2 / 9.9Missense obs/exp: 105 / 174.7Syn Z: -0.15
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveSLC25A4-related mitochondrial diseaseOTHERAR
strongSLC25A4-related Fontaine progeroid syndromeOTHERAD
strongSLC25A4-related severe early-onset mitochondrial disease and loss of mitochondrial DNA copy numberOTHERAD
Mechanism Note (variant-dependent)
DNLOF— mechanism depends on specific variant

Mitochondrial ADP/ATP carrier. Dominant DN variants cause adPEO with mtDNA deletions. Recessive LOF causes mitochondrial myopathy and cardiomyopathy. Mechanism depends on inheritance pattern.

References:PMID:10942118
DN
0.82top 10%
GOF
0.7126th %ile
LOF
0.3550th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median · 1 literature citation
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

DNHowever, expression of aac2(A128P) results in depolarization, structural swelling and disintegration of mitochondria, and ultimately an arrest of cell growth in a dominant-negative manner.PMID:12140186

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SLC25A4 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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