SLC25A15

solute carrier family 25 member 15, the group of Solute carrier family 25|MicroRNA protein coding host genes

Basic information

Region (hg38): 13:40789412-40812460

Previous symbols: [ "ORNT1", "HHH" ]

Links

ENSG00000102743NCBI:10166OMIM:603861HGNC:10985Uniprot:Q9Y619AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ornithine translocase deficiency (Definitive), mode of inheritance: AR
  • ornithine translocase deficiency (Strong), mode of inheritance: AR
  • ornithine translocase deficiency (Supportive), mode of inheritance: AR
  • ornithine translocase deficiency (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hyperornithinemia-hyperammonemia-homocitrullinemia syndromeARBiochemicalDietary (eg, low protein diet,) and medical therapy (eg, with ornithine, citrulline and phenylbutyrate sodium), including during pregnancy, has been reported as beneficialBiochemical; Gastrointestinal; Neurologic5782534; 3091924; 3116497; 3670619; 3106719; 3407856; 2222247; 10369256; 11355015; 11552031; 16940241; 18978333; 19242930; 20574716; 22465082; 25135652

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A15 gene.

  • Hyperornithinemia-hyperammonemia-homocitrullinuria_syndrome (352 variants)
  • Inborn_genetic_diseases (38 variants)
  • not_provided (36 variants)
  • not_specified (21 variants)
  • SLC25A15-related_disorder (8 variants)
  • Intellectual_disability (2 variants)
  • Hereditary_breast_ovarian_cancer_syndrome (1 variants)
  • Abnormal_facial_shape (1 variants)
  • Cardiac_arrhythmia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A15 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014252.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
117
clinvar
121
missense
2
clinvar
14
clinvar
94
clinvar
8
clinvar
1
clinvar
119
nonsense
6
clinvar
9
clinvar
15
start loss
1
1
frameshift
18
clinvar
16
clinvar
1
clinvar
35
splice donor/acceptor (+/-2bp)
2
clinvar
10
clinvar
12
Total 28 50 99 125 1

Highest pathogenic variant AF is 0.0000557604

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC25A15protein_codingprotein_codingENST00000338625 620700
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.70e-70.3611257050431257480.000171
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1011601640.9780.000009801946
Missense in Polyphen6163.1870.96539717
Synonymous-0.5607064.31.090.00000415606
Loss of Function0.5561113.20.8357.24e-7164

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004080.000408
Ashkenazi Jewish0.00009920.0000992
East Asian0.0007610.000761
Finnish0.0001390.000139
European (Non-Finnish)0.00006150.0000615
Middle Eastern0.0007610.000761
South Asian0.0001960.000196
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Ornithine-citrulline antiporter. Connects the cytosolic and the intramitochondrial reactions of the urea cycle by exchanging cytosolic ornithine with matrix citrulline (PubMed:12807890). The stoichiometry is close to 1:1 (By similarity). {ECO:0000250|UniProtKB:A0A0G2K309, ECO:0000269|PubMed:12807890}.;
Pathway
Argininemia;Hyperornithinemia with gyrate atrophy (HOGA);Creatine deficiency, guanidinoacetate methyltransferase deficiency;L-arginine:glycine amidinotransferase deficiency;Hyperornithinemia-hyperammonemia-homocitrullinuria [HHH-syndrome];Guanidinoacetate Methyltransferase Deficiency (GAMT Deficiency);Citrullinemia Type I;Carbamoyl Phosphate Synthetase Deficiency;Argininosuccinic Aciduria;Urea Cycle;Prolinemia Type II;Prolidase Deficiency (PD);Ornithine Transcarbamylase Deficiency (OTC Deficiency);Arginine and Proline Metabolism;Hyperprolinemia Type I;Hyperprolinemia Type II;Ornithine Aminotransferase Deficiency (OAT Deficiency);Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency);Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Vitamin H (biotin) metabolism;Urea cycle (Consensus)

Intolerance Scores

loftool
0.494
rvis_EVS
0.08
rvis_percentile_EVS
60.09

Haploinsufficiency Scores

pHI
0.165
hipred
N
hipred_score
0.248
ghis
0.445

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.747

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc25a15
Phenotype

Gene ontology

Biological process
urea cycle;mitochondrial L-ornithine transmembrane transport
Cellular component
mitochondrial inner membrane;integral component of membrane
Molecular function
L-ornithine transmembrane transporter activity