SLC25A15

Chr 13AR

solute carrier family 25 member 15

Also known as: D13S327, HHH, LNC-HC, ORC1, ORNT1

The encoded protein transports ornithine across the inner mitochondrial membrane and is essential for the urea cycle, functioning in ammonium detoxification and arginine biosynthesis. Mutations cause hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome through autosomal recessive inheritance. The pathogenic mechanism involves dominant negative effects that disrupt normal mitochondrial ornithine transport.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismARLOEUF 1.381 OMIM phenotype
Clinical SummarySLC25A15
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Gene-Disease Validity (ClinGen)
ornithine translocase deficiency · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📖
GeneReview available — SLC25A15
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
1.38LOEUF
pLI 0.000
Z-score 0.56
OE 0.83 (0.521.38)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.10Z-score
OE missense 0.98 (0.861.11)
160 obs / 163.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.83 (0.521.38)
00.351.4
Missense OE0.98 (0.861.11)
00.61.4
Synonymous OE1.09
01.21.6
LoF obs/exp: 11 / 13.2Missense obs/exp: 160 / 163.6Syn Z: -0.56
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveSLC25A15-related hyperornithinemia-hyperammonemia-homocitrullinuria syndromeLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.79top 25%
GOF
0.6541th %ile
LOF
0.2970th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SLC25A15 · 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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