SLC25A33
Basic information
Region (hg38): 1:9539465-9585173
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (38 variants)
- SLC25A33-related_disorder (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A33 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032315.3. 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 | 5 | |||||
| missense | 37 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 3 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC25A33 | protein_coding | protein_coding | ENST00000302692 | 7 | 45697 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00592 | 0.975 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.835 | 144 | 175 | 0.822 | 0.0000100 | 2038 |
| Missense in Polyphen | 75 | 99.38 | 0.75468 | 1036 | ||
| Synonymous | -0.565 | 70 | 64.2 | 1.09 | 0.00000359 | 658 |
| Loss of Function | 2.04 | 6 | 14.4 | 0.418 | 6.85e-7 | 194 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000930 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000108 | 0.000105 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000659 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mitochondrial transporter that imports/exports pyrimidine nucleotides into and from mitochondria (PubMed:25320081). Transports preferentially uracil, thymine, and cytosine (deoxy)nucleoside di- and triphosphates by an antiport mechanism (PubMed:25320081). Also transports guanine but not adenine (deoxy)nucleotides (PubMed:25320081). Is inhibited strongly by pyridoxal 5'-phosphate, 4,7-diphenyl-1,10- phenanthroline, tannic acid, and mercurials (mercury dichloride, mersalyl acid, p-hydroxymercuribenzoate) (PubMed:25320081). Participates in mitochondrial genome maintenance, regulation of mitochondrial membrane potential and mitochondrial respiration (PubMed:20453889). Upon INS or IGF1 stimulation regulates cell growth and proliferation by controlling mitochondrial DNA replication and transcription, the ratio of mitochondria-to nuclear-encoded components of the electron transport chain resulting in control of mitochondrial ROS production (PubMed:20453889, PubMed:17596519). Participates in dendritic cell endocytosis and may associate with mitochondrial oxidative phosphorylation (PubMed:14715278). {ECO:0000269|PubMed:14715278, ECO:0000269|PubMed:17596519, ECO:0000269|PubMed:20453889, ECO:0000269|PubMed:25320081}.;
Recessive Scores
- pRec
- 0.0876
Intolerance Scores
- loftool
- 0.424
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 39.95
Haploinsufficiency Scores
- pHI
- 0.110
- hipred
- Y
- hipred_score
- 0.699
- ghis
- 0.535
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.123
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc25a33
- Phenotype
Gene ontology
- Biological process
- mitochondrial genome maintenance;regulation of oxidative phosphorylation;mitochondrial transcription;pyrimidine nucleotide transport;mitochondrion organization;positive regulation of cell population proliferation;positive regulation of cell growth;mitochondria-nucleus signaling pathway;cellular response to insulin stimulus;mitochondrial respiratory chain complex III assembly;regulation of mitochondrial membrane potential;regulation of cell cycle arrest;regulation of reactive oxygen species biosynthetic process;cellular response to insulin-like growth factor stimulus;pyrimidine nucleotide import into mitochondrion
- Cellular component
- mitochondrial inner membrane;integral component of membrane;mitochondrial membrane
- Molecular function
- pyrimidine nucleotide transmembrane transporter activity