SLC25A17
protein-codingsolute carrier family 25 member 17, the group of Solute carrier family 25|MicroRNA protein coding host genes
Gene summary
This gene encodes a peroxisomal membrane protein that belongs to the family of mitochondrial solute carriers. It is expressed in the liver, and is likely involved in transport. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC25A17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006358.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 51 | 2 | 53 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 54 | 2 | 0 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006349.1 | 9 | MANE Select | |
| Ensembl | ENSP00000390722.2 | 9 | MANE Select | |
| RefSeq | NP_001269655.1 | 8 | Standard | |
| RefSeq | NP_001269656.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Metabolism of lipids
- Alpha-oxidation of phytanate
- Purine metabolism
- Peroxisomal lipid metabolism
Biological Process
- fatty acid alpha-oxidation
- fatty acid beta-oxidation
- ADP transport
- ATP transport
- fatty acid transport
Molecular Function
- adenine nucleotide transmembrane transporter activity
- ATP transmembrane transporter activity
- protein binding
- ADP transmembrane transporter activity
- coenzyme A transmembrane transporter activity
Cellular Component
- peroxisome
- peroxisomal membrane
- integral component of peroxisomal membrane
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000435456
- Coding exons
- 9
- Length
- 49770
- Individuals with no LoFs
- 125697
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 51
- Defined
- 125748
- p
- 0.000203
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.538 | 152 | 172 | 0.885 | 0.00000929 | 1968 |
| Missense (PolyPhen) | 59 | 67.974 | 0.86798 | 819 | ||
| Synonymous | 0.349 | 59 | 62.5 | 0.944 | 0.00000312 | 628 |
| Loss of Function | 1.70 | 10 | 17.8 | 0.563 | 9.82e-7 | 196 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00079 | 0.00079 | rare |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Peroxisomal transporter for multiple cofactors like coenzyme A (CoA), flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) and nucleotide adenosine monophosphate (AMP), and to a lesser extent for nicotinamide adenine dinucleotide (NAD(+)), adenosine diphosphate (ADP) and adenosine 3',5'- diphosphate (PAP). May catalyze the transport of free CoA, FAD and NAD(+) from the cytosol into the peroxisomal matrix by a counter- exchange mechanism. Inhibited by pyridoxal 5'-phosphate and bathophenanthroline in vitro. {ECO:0000269|PubMed:12445829, ECO:0000269|PubMed:22185573}.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.574
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 57.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.857
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |