SLC25A42

Summary

SLC25A42 (solute carrier family 25 member 42, HGNC:28380) is a protein-coding gene on chromosome 19p13.11, encoding Mitochondrial coenzyme A transporter SLC25A42 (Q86VD7). Mitochondrial carrier mediating the transport of coenzyme A (CoA) in mitochondria in exchange for intramitochondrial (deoxy)adenine nucleotides and adenosine 3’,5’-diphosphate.

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.

Source: NCBI Gene 284439 — RefSeq curated summary.

At a glance

• Gene–disease (curated): metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Strong, GenCC)
• Clinical variants (ClinVar): 197 total — 1 pathogenic, 2 likely-pathogenic
• Phenotypes (HPO): 27
• MANE Select transcript: NM_178526

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28380
Approved symbol	SLC25A42
Name	solute carrier family 25 member 42
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC26694
Ensembl gene	ENSG00000181035
Ensembl biotype	protein_coding
OMIM	610823
Entrez	284439

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 18 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000318596, ENST00000594070, ENST00000596819, ENST00000597661, ENST00000600251, ENST00000600275, ENST00000857041, ENST00000857042, ENST00000857043, ENST00000857044, ENST00000857045, ENST00000857046, ENST00000857047, ENST00000857048, ENST00000857049, ENST00000857050, ENST00000857051, ENST00000911412, ENST00000957719, ENST00000957720, ENST00000957721, ENST00000957722, ENST00000957723

RefSeq mRNA: 2 — MANE Select: NM_178526 NM_001321544, NM_178526

CCDS: CCDS32966

Canonical transcript exons

ENST00000318596 — 8 exons

Exon	Start	End
ENSE00001219466	19110569	19113030
ENSE00001429438	19063994	19064115
ENSE00003462302	19104913	19104938
ENSE00003482528	19105561	19105727
ENSE00003496907	19107894	19108045
ENSE00003539913	19101781	19101886
ENSE00003600425	19106269	19106385
ENSE00003644848	19096091	19096205

Expression profiles

Bgee: expression breadth ubiquitous, 225 present calls, max score 93.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.4975 / max 74.9422, expressed in 1539 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174762	5.6754	1478
174768	0.2924	178
174767	0.2226	116
174770	0.1929	99
174769	0.0653	25
174766	0.0178	7
174763	0.0165	7
174765	0.0111	4
174764	0.0034	2

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	93.53	gold quality
gastrocnemius	UBERON:0001388	91.17	gold quality
vena cava	UBERON:0004087	90.56	silver quality
muscle of leg	UBERON:0001383	90.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.74	gold quality
liver	UBERON:0002107	89.68	gold quality
right lobe of thyroid gland	UBERON:0001119	89.63	gold quality
left lobe of thyroid gland	UBERON:0001120	89.58	gold quality
thyroid gland	UBERON:0002046	89.44	gold quality
body of tongue	UBERON:0011876	88.83	gold quality
adult mammalian kidney	UBERON:0000082	88.39	gold quality
mucosa of transverse colon	UBERON:0004991	88.07	gold quality
renal medulla	UBERON:0000362	87.80	gold quality
tongue	UBERON:0001723	87.53	gold quality
oocyte	CL:0000023	87.11	gold quality
apex of heart	UBERON:0002098	87.03	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	86.79	gold quality
granulocyte	CL:0000094	86.72	gold quality
cortex of kidney	UBERON:0001225	86.65	gold quality
kidney epithelium	UBERON:0004819	86.61	silver quality
left ovary	UBERON:0002119	86.51	gold quality
bone marrow cell	CL:0002092	86.38	gold quality
skeletal muscle tissue	UBERON:0001134	86.28	gold quality
right ovary	UBERON:0002118	86.18	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.95	gold quality
superior surface of tongue	UBERON:0007371	85.89	silver quality
kidney	UBERON:0002113	85.61	gold quality
left ventricle myocardium	UBERON:0006566	85.61	gold quality
nucleus accumbens	UBERON:0001882	85.53	gold quality
cerebellar hemisphere	UBERON:0002245	85.53	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-10	no	84.99
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

114 targeting SLC25A42, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-4762-5P	99.57	68.54	1424

Literature-anchored findings (GeneRIF, showing 4)

• The main physiological role of SLC25A42 is to import CoA into mitochondria in exchange for intramitochondrial (deoxy)adenine nucleotides and adenosine 3’,5’-diphosphate (PMID:19429682)
• Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)
• our report confirms the link between SLC25A42 and mitochondrial disease in humans, and suggests that pathogenic variants in SLC25A42 should be interpreted with the understanding that the associated phenotype may be highly variable. (PMID:29327420)
• Novel role of host protein SLC25A42 in the HIV-1 reactivation of latent HIV-1 provirus. (PMID:38244193)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc25a42	ENSDARG00000099368
mus_musculus	Slc25a42	ENSMUSG00000002346
rattus_norvegicus	Slc25a42	ENSRNOG00000020345
drosophila_melanogaster	DPCoAC	FBGN0067783
caenorhabditis_elegans	slc-25A42	WBGENE00009666

Paralogs (49): SLC25A13 (ENSG00000004864), SLC25A5 (ENSG00000005022), SLC25A39 (ENSG00000013306), SLC25A40 (ENSG00000075303), SLC25A3 (ENSG00000075415), SLC25A43 (ENSG00000077713), SLC25A24 (ENSG00000085491), SLC25A1 (ENSG00000100075), SLC25A17 (ENSG00000100372), SLC25A14 (ENSG00000102078), SLC25A15 (ENSG00000102743), SLC25A11 (ENSG00000108528), UCP1 (ENSG00000109424), SLC25A36 (ENSG00000114120), SLC25A12 (ENSG00000115840), SLC25A2 (ENSG00000120329), SLC25A51 (ENSG00000122696), SLC25A16 (ENSG00000122912), SLC25A35 (ENSG00000125434), SLC25A19 (ENSG00000125454), SLC25A23 (ENSG00000125648), SLC25A47 (ENSG00000140107), SLC25A52 (ENSG00000141437), SLC25A38 (ENSG00000144659), SLC25A26 (ENSG00000144741), SLC25A48 (ENSG00000145832), SLC25A37 (ENSG00000147454), SLC25A25 (ENSG00000148339), SLC25A31 (ENSG00000151475), SLC25A4 (ENSG00000151729), SLC25A27 (ENSG00000153291), SLC25A28 (ENSG00000155287), SLC25A44 (ENSG00000160785), SLC25A45 (ENSG00000162241), SLC25A34 (ENSG00000162461), SLC25A32 (ENSG00000164933), SLC25A6 (ENSG00000169100), SLC25A33 (ENSG00000171612), SLC25A30 (ENSG00000174032), UCP3 (ENSG00000175564)

Protein

Protein identifiers

Mitochondrial coenzyme A transporter SLC25A42 — Q86VD7 (reviewed: Q86VD7)

Alternative names: Solute carrier family 25 member 42

All UniProt accessions (1): Q86VD7

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial carrier mediating the transport of coenzyme A (CoA) in mitochondria in exchange for intramitochondrial (deoxy)adenine nucleotides and adenosine 3’,5’-diphosphate.

Subcellular location. Mitochondrion inner membrane.

Disease relevance. Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (MECREN) [MIM:618416] An autosomal recessive disease characterized by muscle weakness, developmental delay, lactic acidosis, and encephalopathy. The severity of the clinical manifestations is highly variable even within affected individuals of the same family, ranging from asymptomatic lactic acidosis to severe developmental regression, epilepsy, intellectual disability, metabolic crisis, and multiorgan involvement. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the mitochondrial carrier (TC 2.A.29) family.

RefSeq proteins (2): NP_001308473, NP_848621* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002067	MCP	Family
IPR002167	GDC-like	Family
IPR014762	DNA_mismatch_repair_CS	Conserved_site
IPR018108	MCP_transmembrane	Repeat
IPR023395	MCP_dom_sf	Homologous_superfamily

Pfam: PF00153

Catalyzed reactions (Rhea), 6 shown:

• ADP(in) + ATP(out) = ADP(out) + ATP(in) (RHEA:34999)
• ADP(out) + CoA(in) = ADP(in) + CoA(out) (RHEA:72839)
• 3’-dephospho-CoA(in) + ADP(out) = 3’-dephospho-CoA(out) + ADP(in) (RHEA:72843)
• adenosine 3’,5’-bisphosphate(in) + ADP(out) = adenosine 3’,5’-bisphosphate(out) + ADP(in) (RHEA:72847)
• AMP(in) + ADP(out) = AMP(out) + ADP(in) (RHEA:72851)
• dADP(in) + ADP(out) = dADP(out) + ADP(in) (RHEA:72855)

UniProt features (13 total): transmembrane region 6, sequence variant 3, repeat 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VD7-F1	90.95	0.78

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-199220	Vitamin B5 (pantothenate) metabolism
R-HSA-1430728	Metabolism
R-HSA-196849	Metabolism of water-soluble vitamins and cofactors
R-HSA-196854	Metabolism of vitamins and cofactors

MSigDB gene sets: 179 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_NUCLEOTIDE_TRANSPORT, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOBP_AMIDE_METABOLIC_PROCESS, GOMF_NUCLEOBASE_CONTAINING_COMPOUND_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, GOBP_SULFUR_COMPOUND_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_PURINE_NUCLEOTIDE_TRANSPORT, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_CATION_TRANSPORT, FAELT_B_CLL_WITH_VH3_21_UP, GOBP_CARBOHYDRATE_DERIVATIVE_TRANSPORT

GO Biological Process (6): ADP transport (GO:0015866), ATP transport (GO:0015867), pantothenate metabolic process (GO:0015939), coenzyme A transmembrane transport (GO:0035349), AMP transport (GO:0080121), transmembrane transport (GO:0055085)

GO Molecular Function (6): ATP transmembrane transporter activity (GO:0005347), ADP transmembrane transporter activity (GO:0015217), coenzyme A transmembrane transporter activity (GO:0015228), ADP phosphatase activity (GO:0043262), AMP transmembrane transporter activity (GO:0080122), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Metabolism of water-soluble vitamins and cofactors	1
Metabolism of vitamins and cofactors	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
purine ribonucleotide transport	3
adenine nucleotide transport	3
adenine nucleotide transmembrane transporter activity	3
purine ribonucleotide transmembrane transporter activity	3
intracellular membrane-bounded organelle	2
modified amino acid metabolic process	1
monocarboxylic acid metabolic process	1
coenzyme A transport	1
purine-containing compound transmembrane transport	1
transport	1
cellular process	1
ATP transport	1
ADP transport	1
organophosphate ester transmembrane transporter activity	1
nucleobase-containing compound transmembrane transporter activity	1
coenzyme A transmembrane transport	1
sulfur compound transmembrane transporter activity	1
nucleoside diphosphate phosphatase activity	1
AMP transport	1
binding	1
cytoplasm	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1851 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC25A42	TMEM161A	Q9NX61	591
SLC25A42	NR2C2AP	Q86WQ0	489
SLC25A42	SLC35E1	Q96K37	470
SLC25A42	NUDT8	Q8WV74	463
SLC25A42	TMEM94	Q12767	448
SLC25A42	KLHDC8B	Q8IXV7	441
SLC25A42	APPL2	Q8NEU8	432
SLC25A42	SLC33A1	O00400	419
SLC25A42	CIB3	Q96Q77	403
SLC25A42	CHERP	Q8IWX8	403
SLC25A42	SLC25A53	Q5H9E4	388
SLC25A42	SUGP1	Q8IWZ8	381
SLC25A42	EXOC6B	Q9Y2D4	373
SLC25A42	PANK2	Q9BZ23	361
SLC25A42	PUS1	Q9Y606	358

IntAct

22 interactions, top by confidence:

A	B	Type	Score
KRTAP10-8	SLC25A42	psi-mi:“MI:0915”(physical association)	0.560
KRT31	SLC25A42	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	SLC25A42	psi-mi:“MI:0915”(physical association)	0.560
KRT34	SLC25A42	psi-mi:“MI:0915”(physical association)	0.560
SLC25A42	HSPA8	psi-mi:“MI:0915”(physical association)	0.400
GRN	SLC25A42	psi-mi:“MI:0915”(physical association)	0.400
PB2	SEC15L3	psi-mi:“MI:0914”(association)	0.350
HLA-DRA	TMEM223	psi-mi:“MI:0914”(association)	0.350
RAMP2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
SLC22A4	RTL8C	psi-mi:“MI:0914”(association)	0.350
OR7A5	UBE4B	psi-mi:“MI:0914”(association)	0.350
SLC39A2	AGPAT2	psi-mi:“MI:0914”(association)	0.350
HDAC11	AGPS	psi-mi:“MI:0914”(association)	0.350
SLC25A42	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.000
SLC25A42	KRT31	psi-mi:“MI:0915”(physical association)	0.000
SLC25A42	MTUS2	psi-mi:“MI:0915”(physical association)	0.000
SLC25A42	KRT34	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): SLC25A42 (Affinity Capture-RNA), SLC25A42 (Two-hybrid), SLC25A42 (Two-hybrid), SLC25A42 (Two-hybrid), KRTAP10-8 (Two-hybrid), SLC25A42 (Affinity Capture-MS), SLC25A42 (Affinity Capture-MS), SLC25A42 (Affinity Capture-MS), SLC25A42 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), GARS (Cross-Linking-MS (XL-MS)), SLC25A42 (Co-fractionation), SLC25A42 (Co-fractionation), SLC25A42 (Co-fractionation), SLC25A42 (Co-fractionation)

ESM2 similar proteins: A0A1D6N272, A1DI57, A2R5A0, A4RF23, A6RF73, A6SL61, A7ER02, B4FIJ0, G3XP90, G3YAF3, G3YD89, O04619, O13844, O65023, P0C546, P16260, Q01888, Q05AQ3, Q0CEN9, Q0P483, Q0UUH1, Q1E7P0, Q1LZB3, Q29RM1, Q2UCW8, Q3TZX3, Q4X022, Q5AVW1, Q5IS35, Q5NVC1, Q5PQ27, Q6AYL0, Q6P036, Q7K566, Q7S2H8, Q86VD7, Q8BZ09, Q8C0K5, Q8R0Y8, Q8RWA5

Diamond homologs: A0A1D6N272, A1DI57, A2ASZ8, A2CEQ0, A2R5A0, A3LVX1, A4RF23, A5DIS9, A5DX39, A6RF73, A6SL61, A7ER02, A7TIQ0, B4FIJ0, F4JU70, O04619, O94370, O95847, P29518, P49382, Q05AQ3, Q0CEN9, Q0P483, Q0UUH1, Q1E7P0, Q29RM1, Q2HFL6, Q2UCW8, Q3ZBJ8, Q4X022, Q54VS7, Q552L9, Q55E45, Q59Q36, Q5AVW1, Q5IS35, Q5NVC1, Q5PQ27, Q5XH95, Q5XHA0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

197 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	2
Uncertain significance	73
Likely benign	98
Benign	10

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
627557	NM_178526.5(SLC25A42):c.380+2T>A	Pathogenic
2276907	NM_178526.5(SLC25A42):c.623_624del (p.Thr207_Tyr208insTer)	Likely pathogenic
598758	NM_178526.5(SLC25A42):c.309C>G (p.Tyr103Ter)	Likely pathogenic

SpliceAI

1317 predictions. Top by Δscore:

Variant	Effect	Δscore
19:19101776:TGCA:T	acceptor_loss	1.0000
19:19101777:GCA:G	acceptor_loss	1.0000
19:19101778:CA:C	acceptor_loss	1.0000
19:19101779:A:AG	acceptor_gain	1.0000
19:19101779:A:C	acceptor_loss	1.0000
19:19101779:AGC:A	acceptor_gain	1.0000
19:19101779:AGCGT:A	acceptor_gain	1.0000
19:19101780:G:GA	acceptor_gain	1.0000
19:19101780:GC:G	acceptor_gain	1.0000
19:19101780:GCG:G	acceptor_gain	1.0000
19:19101780:GCGT:G	acceptor_gain	1.0000
19:19101780:GCGTG:G	acceptor_gain	1.0000
19:19101884:AAGGT:A	donor_loss	1.0000
19:19101885:AGG:A	donor_loss	1.0000
19:19101887:G:GG	donor_gain	1.0000
19:19101887:GTAA:G	donor_loss	1.0000
19:19101888:T:G	donor_loss	1.0000
19:19105558:CAG:C	acceptor_loss	1.0000
19:19105559:A:AG	acceptor_gain	1.0000
19:19105559:AG:A	acceptor_gain	1.0000
19:19105560:G:GG	acceptor_gain	1.0000
19:19105560:GG:G	acceptor_gain	1.0000
19:19105560:GGA:G	acceptor_gain	1.0000
19:19105683:G:GT	donor_gain	1.0000
19:19105683:GGA:G	donor_gain	1.0000
19:19105684:GAG:G	donor_gain	1.0000
19:19105686:G:GG	donor_gain	1.0000
19:19105707:C:G	donor_gain	1.0000
19:19105723:GGAGA:G	donor_gain	1.0000
19:19105724:GAGA:G	donor_gain	1.0000

AlphaMissense

2025 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:19107962:G:A	G189E	1.000
19:19101866:G:C	R56P	0.999
19:19105622:G:A	G92E	0.999
19:19105661:C:A	A105D	0.999
19:19105669:T:C	F108L	0.999
19:19105671:C:A	F108L	0.999
19:19105671:C:G	F108L	0.999
19:19106322:C:A	A145D	0.999
19:19101818:G:A	G40E	0.998
19:19101827:C:A	A43D	0.998
19:19101830:G:A	G44D	0.998
19:19101839:C:A	A47D	0.998
19:19101857:C:A	P53H	0.998
19:19101857:C:G	P53R	0.998
19:19101872:A:T	K58I	0.998
19:19101873:A:C	K58N	0.998
19:19101873:A:T	K58N	0.998
19:19105615:T:A	W90R	0.998
19:19105615:T:C	W90R	0.998
19:19105621:G:A	G92R	0.998
19:19105621:G:C	G92R	0.998
19:19105622:G:T	G92V	0.998
19:19105626:C:A	N93K	0.998
19:19105626:C:G	N93K	0.998
19:19105631:C:A	A95D	0.998
19:19105660:G:C	A105P	0.998
19:19105670:T:C	F108S	0.998
19:19105675:G:C	A110P	0.998
19:19106345:G:C	D153H	0.998
19:19106346:A:G	D153G	0.998

dbSNP variants (sampled 300 via entrez): RS1000027315 (19:19102845 G>C), RS1000108975 (19:19110410 G>A), RS1000180716 (19:19097586 C>G,T), RS1000188639 (19:19104046 G>C), RS1000217154 (19:19086974 G>A), RS1000237873 (19:19103784 T>A,C), RS1000290224 (19:19091236 C>A,T), RS1000466347 (19:19110633 C>G,T), RS1000502199 (19:19073091 C>T), RS1000508472 (19:19077627 C>T), RS1000560287 (19:19077965 C>T), RS1000632029 (19:19077606 A>G), RS1000638612 (19:19091775 G>T), RS1000809106 (19:19065729 G>C), RS1000870524 (19:19097919 C>T)

Disease associations

OMIM: gene MIM:610823 | disease phenotypes: MIM:618416

GenCC curated gene-disease

Disease	Classification	Inheritance
metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression	Strong	Autosomal recessive

Mondo (2): inborn mitochondrial myopathy (MONDO:0009637), metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (MONDO:0032736)

Orphanet (1): Mitochondrial myopathy (Orphanet:206966)

HPO phenotypes

27 total (27 of 27 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000750	Delayed speech and language development
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001260	Dysarthria
HP:0001263	Global developmental delay
HP:0001266	Choreoathetosis
HP:0001270	Motor delay
HP:0001290	Generalized hypotonia
HP:0001332	Dystonia
HP:0001987	Hyperammonemia
HP:0002151	Increased circulating lactate concentration
HP:0002359	Frequent falls
HP:0002376	Developmental regression
HP:0002650	Scoliosis
HP:0003128	Lactic acidosis
HP:0003200	Ragged-red muscle fibers
HP:0003201	Rhabdomyolysis
HP:0003236	Elevated circulating creatine kinase concentration
HP:0003388	Easy fatigability
HP:0003593	Infantile onset
HP:0003688	Cytochrome C oxidase-negative muscle fibers
HP:0003701	Proximal muscle weakness
HP:0003738	Exercise-induced myalgia
HP:0025336	Delayed ability to sit
HP:0030319	Weakness of facial musculature
HP:0031936	Delayed ability to walk

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D017240	Mitochondrial Myopathies	C05.651.460; C10.668.491.500; C18.452.660.560

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC25 mitochondrial vitamin and co-factor carriers subfamily

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Aflatoxin B1	decreases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Acetaminophen	decreases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects binding, increases expression, affects expression, increases reaction	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	increases expression	1

Cellosaurus cell lines

5 cell lines: 4 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D4SN	HuH7-SLC25A42-KO-c1	Cancer cell line	Male
CVCL_D4SP	HuH7-SLC25A42-KO-c2	Cancer cell line	Male
CVCL_D9RT	Ubigene HEK293 SLC25A42 KO	Transformed cell line	Female
CVCL_TM49	HAP1 SLC25A42 (-) 1	Cancer cell line	Male
CVCL_XT05	HAP1 SLC25A42 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

40 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT03323749	PHASE3	TERMINATED	A Trial to Evaluate Safety and Efficacy of Elamipretide Primary Mitochondrial Myopathy Followed by Open-Label Extension
NCT05162768	PHASE3	COMPLETED	Study to Evaluate Efficacy and Safety of Elamipretide in Subjects With Primary Mitochondrial Disease From Nuclear DNA Mutations (nPMD)
NCT00457314	PHASE2	UNKNOWN	The Effects of Exercise Versus Inactivity on People With Mitochondrial Muscle Disease
NCT02255422	PHASE2	COMPLETED	RTA 408 Capsules in Patients With Mitochondrial Myopathy - MOTOR
NCT02909400	PHASE2	COMPLETED	The KHENERGY Study
NCT04165239	PHASE2	COMPLETED	The KHENERGYZE Study
NCT04535609	PHASE2	COMPLETED	An Efficacy and Safety Study of 24 Week Treatment With Mavodelpar (REN001) in Primary Mitochondrial Myopathy Patients
NCT04641962	PHASE2	TERMINATED	A Study to Evaluate ASP0367 in Participants With Primary Mitochondrial Myopathy
NCT05590468	PHASE2	ACTIVE_NOT_RECRUITING	A Study to Evaluate Vitamin B3 Derivative to Treat Mitochondrial Myopathy
NCT05962333	PHASE2	UNKNOWN	Effect and Safety MABs Administration m.3243A>G Mutation Carriers
NCT06754098	PHASE2	RECRUITING	Doxecitin and Doxribthymine in Adult Subjects With Thymidine Kinase 2 (TK2) Deficiency
NCT03862846	PHASE1	TERMINATED	A Study of the Safety of REN001 in Patients With Primary Mitochondrial Myopathy
NCT03888716	PHASE1	COMPLETED	A Phase Ia/Ib, SAD and MAD Study of of KL1333 in Healthy Subjects and Patients With Primary Mitochondrial Disease
NCT04086329	PHASE1	RECRUITING	Validation of Oxygen Nanosensor in Mitochondrial Myopathy
NCT05063721	PHASE1	COMPLETED	MABs Therapy m.3243A>G Mutation Carriers
NCT05569122	PHASE1	RECRUITING	Applying pGz in Mitochondrial Disease
NCT06819683	PHASE1	RECRUITING	Validation of Nanosensor Oxygen Measurement
NCT05267574	PHASE2/PHASE3	TERMINATED	An Open Label, Long Term Safety Study of REN001 in Primary Mitochondrial Myopathy Patients (Stride Ahead)
NCT02367014	PHASE1/PHASE2	COMPLETED	Safety, Tolerability, and Efficacy of MTP-131 for the Treatment of Mitochondrial Myopathy
NCT06051448	PHASE1/PHASE2	COMPLETED	Promoting Resilience in Stress Management (PRISM) and Clinical-focused Narrative (CFN) Pilot in Adults With Primary Mitochondrial Disease (PMD).
NCT00004353	Not specified	COMPLETED	Study of the Metabolism of Pyruvate and Related Problems in Patients With Lactic Acidemia
NCT00004770	Not specified	COMPLETED	Pilot Compassionate Use Study of Thioctic Acid Treatment in Mitochondrial Myopathy
NCT02375438	Not specified	COMPLETED	Nutritional Assessment in Mitochondrial Cytopathy
NCT02895789	Not specified	COMPLETED	Oxidative Capacity and Exercise Tolerance in Ambulatory SMA
NCT03432871	Not specified	COMPLETED	Nicotinamide Riboside and Mitochondrial Biogenesis
NCT03513835	Not specified	COMPLETED	Diagnostic Screening Tests and Potential Biomarkers in Mitochondrial Myopathies
NCT03728777	Not specified	COMPLETED	Resveratrol Supplementation in Patients With Mitochondrial Myopathies and Skeletal Muscle Fatty Acid Oxidation Disorders
NCT03973203	Not specified	COMPLETED	Niacin Supplementation in Healthy Controls and Mitochondrial Myopathy Patients
NCT04538521	Not specified	COMPLETED	NiaMIT Continuation With Early-stage Mitochondrial Myopathy Patients
NCT05012358	Not specified	COMPLETED	Genomic Profiling of Mitochondrial Disease - Imaging Analysis for Precise Mitochondrial Medicine
NCT05199246	Not specified	COMPLETED	Assessment of Safety and Acute Effects of a Lower-limb Powered Dermoskeleton in Patients With Neuromuscular Disorders
NCT05199740	Not specified	RECRUITING	mtDNA Mutation Load Analysis in Mesoangioblasts
NCT05200702	Not specified	COMPLETED	Assessment of Safety and Acute Effects of a Knee-hip Powered Soft Exoskeleton in Patients With Neuromuscular Disorders
NCT05346627	Not specified	RECRUITING	Home Based Personalized Training and Video Consultation in Mitochondrial Myopathies: Study of Efficacy and Tolerance.
NCT05554835	Not specified	RECRUITING	Global Registry and Natural History Study for Mitochondrial Disorders
NCT06080568	Not specified	COMPLETED	Human Mitochondrial Stress-driven Obesity Resistance
NCT06080581	Not specified	COMPLETED	Mitochondrial Dysfunctions Driving Insulin Resistance
NCT06080594	Not specified	COMPLETED	Exercise-mediated Rescue of Mitochondrial Dysfunctions Driving Insulin Resistance
NCT07450690	Not specified	RECRUITING	Exercise Training Effects on Muscle Function in Adults With Mitochondrial Myopathy
NCT07478172	Not specified	RECRUITING	Effects of Whole-body Electrical Muscle Stimulation Exercise on Adults With Neuromuscular Disease