SLC25A2

Chr 5

solute carrier family 25 member 2

Also known as: ORC2, ORNT2

NCBI Gene: 83884ENSG00000120329UniProt: Q9BXI2

This intronless gene encodes a protein that localizes to the mitochondrial inner membrane and likely functions as a transporter of small molecules such as ornithine. This gene is located between the protocadherin beta and gamma gene clusters on chromosome 5. [provided by RefSeq, Dec 2014]

0
Active trials
11
Pathogenic / LP
59
ClinVar variants
1
Pubs (1 yr)
0.7
Missense Z
1.32
LOEUF
Clinical Summary— SLC25A2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 46 VUS of 59 total submissions
📖
GeneReview available — SLC25A2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.32LOEUF
pLI 0.002
Z-score 0.96
OE 0.63 (0.33–1.32)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.66Z-score
OE missense 0.86 (0.75–0.98)
150 obs / 174.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.63 (0.33–1.32)
0≤0.351.4
Missense OE0.86 (0.75–0.98)
0≤0.61.4
Synonymous OE0.91
0≤1.21.6
LoF obs/exp: 5 / 7.9Missense obs/exp: 150 / 174.5Syn Z: 0.60
DNGOF
DN
0.85top 5%
GOF
0.76top 25%
LOF
0.2092th %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
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.

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

ClinVar Variant Classifications

59 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
VUS46
Likely Benign2
11
Pathogenic
46
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
0
0
0
VUS
0
41
5
0
46
Likely Benign
0
0
2
0
2
Benign
0
0
0
0
0
Total04118059

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

SLC25A2 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Biochemical-molecular-genetic biomarkers in the tear film, aqueous humor, and blood of primary open-angle glaucoma patients
Pinazo-Durán MD et al.·Front Med (Lausanne)
2023Cohort
Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus-Brahman crossbred heifers
Hoorn QA et al.·J Anim Sci Biotechnol
2023
Commentary on "CRISPR/Cas9-mediated genome editing reveals 12 testis-enriched genes dispensable for male fertility in mice"
Houston BJ·Asian J Androl
2022
A deep learning model for early risk prediction of heart failure with preserved ejection fraction by DNA methylation profiles combined with clinical features
Zhao X et al.·Clin Epigenetics
2022Functional
Characterizing Early Cardiac Metabolic Programming via 30% Maternal Nutrient Reduction during Fetal Development in a Non-Human Primate Model
Pereira SP et al.·Int J Mol Sci
2023Functional
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients