SLC25A42
Basic information
Region (hg38): 19:19063994-19113030
Links
Phenotypes
GenCC
Source:
- metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Moderate), mode of inheritance: AR
- metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Strong), mode of inheritance: AR
- metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Cardiovascular; Musculoskeletal; Neurologic; Renal | 26541337; 29327420; 29923093 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (153 variants)
- Inborn_genetic_diseases (33 variants)
- SLC25A42-related_disorder (3 variants)
- Metabolic_crises,_recurrent,_with_variable_encephalomyopathic_features_and_neurologic_regression (2 variants)
- Inborn_mitochondrial_myopathy (2 variants)
- SLC25A42-related_mitochondrial_encephalomyopathy (1 variants)
- SLC25A42-related_mitochondrial_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A42 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178526.5. 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 | 53 | 57 | ||||
missense | 64 | 67 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 1 | 3 | 70 | 54 | 3 |
Highest pathogenic variant AF is 0.00000344876
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC25A42 | protein_coding | protein_coding | ENST00000318596 | 7 | 48890 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.489 | 0.510 | 125735 | 0 | 11 | 125746 | 0.0000437 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.10 | 120 | 205 | 0.586 | 0.0000131 | 2003 |
Missense in Polyphen | 42 | 98.963 | 0.4244 | 963 | ||
Synonymous | -0.0695 | 92 | 91.2 | 1.01 | 0.00000595 | 691 |
Loss of Function | 2.82 | 3 | 14.7 | 0.204 | 7.92e-7 | 171 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000185 | 0.000185 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000532 | 0.0000527 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000671 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mitochondrial carrier mediating the transport of coenzyme A (CoA) in mitochondria in exchange for intramitochondrial (deoxy)adenine nucleotides and adenosine 3',5'- diphosphate. {ECO:0000269|PubMed:19429682}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.428
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.263
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.557
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.944
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc25a42
- Phenotype
Zebrafish Information Network
- Gene name
- slc25a42
- Affected structure
- skeletal muscle
- Phenotype tag
- abnormal
- Phenotype quality
- swollen
Gene ontology
- Biological process
- ADP transport;ATP transport;coenzyme A transmembrane transport;AMP transport
- Cellular component
- nucleus;mitochondrion;mitochondrial inner membrane;integral component of membrane
- Molecular function
- ATP transmembrane transporter activity;ADP transmembrane transporter activity;coenzyme A transmembrane transporter activity;adenosine-diphosphatase activity;AMP transmembrane transporter activity