SLC25A29
protein-codingsolute carrier family 25 member 29, the group of Solute carrier family 25
Gene summary
This gene encodes a nuclear-encoded mitochondrial protein that is a member of the large family of solute carrier family 25 (SLC25) mitochondrial transporters. The members of this superfamily are involved in numerous metabolic pathways and cell functions. This gene product was previously reported to be a mitochondrial carnitine-acylcarnitine-like (CACL) translocase (PMID:128829710) or an ornithine transporter (designated ORNT3, PMID:19287344), however, a recent study characterized the main role of this protein as a mitochondrial transporter of basic amino acids, with a preference for arginine and lysine (PMID:24652292). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]
- C14orf69
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.4 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 SLC25A29 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001039355.3. 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 | 3 | 3 | ||||
| missense | 59 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 62 | 3 | 0 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001034444.1 | 4 | MANE Select | |
| Ensembl | ENSP00000352167.3 | 4 | MANE Select | |
| RefSeq | NP_001278742.1 | 1 | Standard | |
| RefSeq | NP_001278743.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Thermogenesis - Homo sapiens (human)
Biological Process
- acyl carnitine transport
- amino acid transport
- ornithine transport
- carnitine transport
- L-histidine transmembrane transport
Molecular Function
- high-affinity arginine transmembrane transporter activity
- high-affinity lysine transmembrane transporter activity
- basic amino acid transmembrane transporter activity
- acyl carnitine transmembrane transporter activity
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359232
- Coding exons
- 4
- Length
- 15437
- Individuals with no LoFs
- 125296
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 60
- Defined
- 125356
- p
- 0.000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.765 | 179 | 210 | 0.852 | 0.0000162 | 1834 |
| Missense (PolyPhen) | 66 | 97.729 | 0.67534 | 865 | ||
| Synonymous | 1.31 | 88 | 105 | 0.837 | 0.00000904 | 680 |
| Loss of Function | 1.22 | 6 | 10.2 | 0.587 | 5.36e-7 | 106 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000077 | 0.000062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.000054 | 0.000046 | rare |
| European (Non-Finnish) | 0.00038 | 0.00032 | rare |
| South Asian | 0.00057 | 0.00052 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine (PubMed:24652292). Can restore ornithine transport in cells lacking the primary mitochondrial ornithine transporter SLC25A15 (PubMed:19287344). Does not transport carnitine nor acylcarnitines (PubMed:24652292). Functions by both counter- exchange and uniport mechanisms (PubMed:24652292). {ECO:0000269|PubMed:19287344, ECO:0000269|PubMed:24652292}.;
Recessive Scores
- pRec
- 0.154
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.153
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |