SLC25A42

solute carrier family 25 member 42, the group of Solute carrier family 25

Basic information

Region (hg38): 19:19063994-19113030

Links

ENSG00000181035NCBI:284439OMIM:610823HGNC:28380Uniprot:Q86VD7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Cardiovascular; Musculoskeletal; Neurologic; Renal26541337; 29327420; 29923093

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A42 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
53
clinvar
2
clinvar
57
missense
1
clinvar
64
clinvar
1
clinvar
1
clinvar
67
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
2
clinvar
3
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total 1 3 70 54 3

Highest pathogenic variant AF is 0.00000344876

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC25A42protein_codingprotein_codingENST00000318596 748890
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4890.5101257350111257460.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.101202050.5860.00001312003
Missense in Polyphen4298.9630.4244963
Synonymous-0.06959291.21.010.00000595691
Loss of Function2.82314.70.2047.92e-7171

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001850.000185
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005320.0000527
Middle Eastern0.000.00
South Asian0.00006710.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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