SLC25A15
Basic information
Region (hg38): 13:40789412-40812460
Previous symbols: [ "ORNT1", "HHH" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome | AR | Biochemical | Dietary (eg, low protein diet,) and medical therapy (eg, with ornithine, citrulline and phenylbutyrate sodium), including during pregnancy, has been reported as beneficial | Biochemical; Gastrointestinal; Neurologic | 5782534; 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
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 117 | 121 | ||||
missense | 14 | 94 | 119 | |||
nonsense | 15 | |||||
start loss | 1 | 1 | ||||
frameshift | 18 | 16 | 35 | |||
splice donor/acceptor (+/-2bp) | 10 | 12 | ||||
Total | 28 | 50 | 99 | 125 | 1 |
Highest pathogenic variant AF is 0.0000557604
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC25A15 | protein_coding | protein_coding | ENST00000338625 | 6 | 20700 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.70e-7 | 0.361 | 125705 | 0 | 43 | 125748 | 0.000171 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.101 | 160 | 164 | 0.978 | 0.00000980 | 1946 |
Missense in Polyphen | 61 | 63.187 | 0.96539 | 717 | ||
Synonymous | -0.560 | 70 | 64.3 | 1.09 | 0.00000415 | 606 |
Loss of Function | 0.556 | 11 | 13.2 | 0.835 | 7.24e-7 | 164 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000408 | 0.000408 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000761 | 0.000761 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.0000615 | 0.0000615 |
Middle Eastern | 0.000761 | 0.000761 |
South Asian | 0.000196 | 0.000196 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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