SLC25A5
Basic information
Region (hg38): X:119468422-119471396
Previous symbols: [ "ANT2" ]
Links
Phenotypes
GenCC
Source:
- intellectual disability (Limited), mode of inheritance: XL
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (11 variants)
- SLC25A5-related_disorder (9 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001152.5. 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 | 10 | |||||
| missense | 10 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 10 | 8 | 5 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC25A5 | protein_coding | protein_coding | ENST00000317881 | 4 | 2920 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.932 | 0.0678 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.65 | 43 | 127 | 0.338 | 0.0000103 | 1910 |
| Missense in Polyphen | 0 | 22.922 | 0 | 484 | ||
| Synonymous | 1.14 | 38 | 48.1 | 0.790 | 0.00000378 | 597 |
| Loss of Function | 2.71 | 0 | 8.56 | 0.00 | 6.89e-7 | 126 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane. As part of the mitotic spindle-associated MMXD complex it may play a role in chromosome segregation. {ECO:0000269|PubMed:20797633}.;
- Pathway
- Huntington,s disease - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Necroptosis - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Electron Transport Chain;Disease;Vpr-mediated induction of apoptosis by mitochondrial outer membrane permeabilization;Host Interactions of HIV factors;HIV Infection;Infectious disease;Metabolism;Regulation of insulin secretion;Vitamin B9 (folate) metabolism;Integration of energy metabolism;Interactions of Vpr with host cellular proteins
(Consensus)
Recessive Scores
- pRec
- 0.499
Intolerance Scores
- loftool
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.337
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.643
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc25a5
- Phenotype
- cellular phenotype;
Zebrafish Information Network
- Gene name
- slc25a5
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- chromosome segregation;positive regulation of cell population proliferation;adenine transport;ADP transport;ATP transport;viral process;regulation of insulin secretion;transmembrane transport;negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;mitochondrion;mitochondrial inner membrane;integral component of plasma membrane;membrane;mitochondrial nucleoid;myelin sheath;membrane raft;MMXD complex
- Molecular function
- RNA binding;ATP:ADP antiporter activity;protein binding;adenine transmembrane transporter activity;ubiquitin protein ligase binding