GeneBe

SLC25A42

protein-coding

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

Gene summary

This gene encodes a solute carrier family 25 protein. Solute carrier family 25 proteins are localized to mitochondria and play critical roles in the transport of molecules across the inner mitochondrial membrane. The encoded protein is a mitochondrial transporter for coenzyme A (CoA) and adenosine 3',5'-diphosphate. [provided by RefSeq, Feb 2012]

MANE transcript

NM_178526.5

Inheritance

AR

ClinVar variants

P:4U:75B:67

Top phenotype

Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr19:19,063,994-19,113,030

External References & Databases

Ensembl (ENSG00000181035)NCBI Gene (284439)OMIM (610823)HGNC:28380GenCCUniProt (Q86VD7)AlphaFoldClinVar (SLC25A42)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~49.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032736

Submitter: G2P

metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032736

Submitter: Labcorp Genetics (formerly Invitae)

metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0032736

Submitter: Ambry Genetics

metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032736

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionAR

Manifestation: Biochemical; Cardiovascular; Musculoskeletal; Neurologic; Renal

Intervention: General

Rationale: 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

Refs: 26541337; 29327420; 29923093Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC25A42 variants in ClinVar

8 Conditions Cataloged
not providedTotal: 170
Inborn genetic diseasesTotal: 34
not specifiedTotal: 14
SLC25A42-related disorderTotal: 5
Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regressionTotal: 2
Inborn mitochondrial myopathyTotal: 2
SLC25A42-related mitochondrial encephalomyopathyTotal: 1
SLC25A42-related mitochondrial disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178526.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
61
clinvar
2
clinvar
 65
missense
1
clinvar
68
clinvar
4
clinvar
 73
nonsense
1
clinvar
1
clinvar
 2
start loss
0
frameshift
1
clinvar
2
clinvar
 3
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
 3
Total1375652146

Highest pathogenic variant AF is 0.0000034487564

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_178526.5RefSeqNP_848621.27MANE Select
ENST00000318596.8EnsemblENSP00000326693.67MANE Select
NM_001321544.2RefSeqNP_001308473.17Standard
ENST00000857041.1EnsemblENSP00000527100.17Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
slc25a42Danio rerio

Structure: skeletal muscle

Quality: swollen

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • ADP transport
  • ATP transport
  • coenzyme A transmembrane transport
  • AMP transport

Molecular Function

  • ATP transmembrane transporter activity
  • ADP transmembrane transporter activity
  • coenzyme A transmembrane transporter activity
  • adenosine-diphosphatase activity
  • AMP transmembrane transporter activity

Cellular Component

  • nucleus
  • mitochondrion
  • mitochondrial inner membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000318596
Coding exons
7
Length
48890
Individuals with no LoFs
125735
Homozygous LoFs
0
Heterozygous LoFs
11
Defined
125746
p
0.0000437
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.101202050.5860.00001312003
Missense (PolyPhen)4298.9630.4244963
Synonymous-0.06959291.21.010.00000595691
Loss of Function2.82314.70.2047.92e-7171

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000530.000053rare
South Asian0.0000670.000065rare
Other00.0absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.944

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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