SLC25A41

Summary

SLC25A41 (solute carrier family 25 member 41, HGNC:28533) is a protein-coding gene on chromosome 19p13.3, encoding Mitochondrial carrier protein SCaMC-3L (Q8N5S1). Calcium-independent ATP-Mg/Pi exchanger that catalyzes the electroneutral exchange of Mg-ATP or free ADP against an hydrogenphosphate and participates in the net transport of adenine nucleotides across the mitochondria inner membrane.

SLC25A41 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).

Source: NCBI Gene 284427 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_173637

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28533
Approved symbol	SLC25A41
Name	solute carrier family 25 member 41
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40442, MGC34725, APC4
Ensembl gene	ENSG00000181240
Ensembl biotype	protein_coding
OMIM	610822
Entrez	284427

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 nonsense_mediated_decay, 1 protein_coding

ENST00000321510, ENST00000458275, ENST00000597558

RefSeq mRNA: 2 — MANE Select: NM_173637 NM_001321298, NM_173637

CCDS: CCDS45937

Canonical transcript exons

ENST00000321510 — 7 exons

Exon	Start	End
ENSE00001262551	6432049	6432204
ENSE00003511571	6429724	6429831
ENSE00003561683	6430009	6430161
ENSE00003578040	6427103	6427250
ENSE00003668630	6426037	6426561
ENSE00003687244	6427334	6427501
ENSE00003894373	6433487	6433763

Expression profiles

Bgee: expression breadth ubiquitous, 147 present calls, max score 82.53.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0148 / max 20.2988, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178637	0.0148	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	82.53	gold quality
cerebellar cortex	UBERON:0002129	82.32	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.99	gold quality
cerebellum	UBERON:0002037	80.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.47	silver quality
putamen	UBERON:0001874	76.79	gold quality
left testis	UBERON:0004533	76.72	gold quality
right testis	UBERON:0004534	76.56	gold quality
nucleus accumbens	UBERON:0001882	75.97	gold quality
caudate nucleus	UBERON:0001873	75.85	gold quality
testis	UBERON:0000473	73.56	gold quality
right frontal lobe	UBERON:0002810	73.51	gold quality
anterior cingulate cortex	UBERON:0009835	72.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.82	gold quality
mucosa of transverse colon	UBERON:0004991	70.82	gold quality
cortical plate	UBERON:0005343	70.18	gold quality
prefrontal cortex	UBERON:0000451	69.96	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	69.67	gold quality
neocortex	UBERON:0001950	68.17	gold quality
amygdala	UBERON:0001876	67.97	gold quality
frontal cortex	UBERON:0001870	67.90	gold quality
mucosa of stomach	UBERON:0001199	67.87	gold quality
brain	UBERON:0000955	66.87	gold quality
cerebral cortex	UBERON:0000956	66.23	gold quality
forebrain	UBERON:0001890	66.02	gold quality
hypothalamus	UBERON:0001898	65.65	gold quality
Ammon’s horn	UBERON:0001954	64.30	gold quality
lower esophagus muscularis layer	UBERON:0035833	64.09	gold quality
lower esophagus	UBERON:0013473	64.02	gold quality
myocardium	UBERON:0002349	63.93	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting SLC25A41, 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-4715-3P	99.98	66.03	670
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-6818-5P	97.50	67.10	1167
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-4750-3P	96.65	64.38	512
HSA-MIR-6762-5P	96.55	64.62	972
HSA-MIR-6845-5P	96.55	64.65	969
HSA-MIR-3135A	96.41	65.30	494
HSA-MIR-2861	95.24	65.47	1056
HSA-MIR-6726-3P	83.39	62.13	46

Literature-anchored findings (GeneRIF, showing 2)

• Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)
• The APC4 subunit is the major SUMO target in the anaphase-promoting complex/cyclosome, containing SUMO acceptor lysines at positions 772 and 798. (PMID:29549242)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slc25a41	ENSMUSG00000011486
rattus_norvegicus	Slc25a41	ENSRNOG00000048853

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 carrier protein SCaMC-3L — Q8N5S1 (reviewed: Q8N5S1)

Alternative names: Mitochondrial ATP-Mg/Pi carrier protein SLC25A41, Small calcium-binding mitochondrial carrier protein 3-like, Solute carrier family 25 member 41

All UniProt accessions (1): Q8N5S1

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-independent ATP-Mg/Pi exchanger that catalyzes the electroneutral exchange of Mg-ATP or free ADP against an hydrogenphosphate and participates in the net transport of adenine nucleotides across the mitochondria inner membrane.

Subcellular location. Mitochondrion inner membrane.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N5S1-1	1	yes
Q8N5S1-2	2

RefSeq proteins (2): NP_001308227, NP_775908* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002067	MCP	Family
IPR018108	MCP_transmembrane	Repeat
IPR023395	MCP_dom_sf	Homologous_superfamily

Pfam: PF00153

Catalyzed reactions (Rhea), 2 shown:

• Mg(2+)(out) + phosphate(in) + ATP(out) = Mg(2+)(in) + phosphate(out) + ATP(in) (RHEA:65840)
• ADP(out) + phosphate(in) + H(+)(out) = ADP(in) + phosphate(out) + H(+)(in) (RHEA:65844)

UniProt features (14 total): transmembrane region 6, repeat 3, splice variant 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N5S1-F1	73.09	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GCANCTGNY_MYOD_Q6, CAGCTG_AP4_Q5, GOBP_NUCLEOTIDE_TRANSPORT, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOMF_NUCLEOBASE_CONTAINING_COMPOUND_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOBP_NUCLEOTIDE_TRANSMEMBRANE_TRANSPORT, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_PURINE_NUCLEOTIDE_TRANSPORT, GOBP_CARBOHYDRATE_DERIVATIVE_TRANSPORT, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_ORGANELLE_INNER_MEMBRANE, chr19p13, GOMF_ORGANOPHOSPHATE_ESTER_TRANSMEMBRANE_TRANSPORTER_ACTIVITY

GO Biological Process (5): ADP transport (GO:0015866), ATP transport (GO:0015867), mitochondrial ADP transmembrane transport (GO:0140021), mitochondrial ATP transmembrane transport (GO:1990544), transmembrane transport (GO:0055085)

GO Molecular Function (2): ATP transmembrane transporter activity (GO:0005347), ADP transmembrane transporter activity (GO:0015217)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
purine ribonucleotide transport	2
adenine nucleotide transport	2
ADP transport	2
purine-containing compound transmembrane transport	2
nucleotide transmembrane transport	2
ATP transport	2
adenine nucleotide transmembrane transporter activity	2
purine ribonucleotide transmembrane transporter activity	2
transport	1
cellular process	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

958 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC25A41	TMEM210	A6NLX4	626
SLC25A41	SMIM9	A6NGZ8	607
SLC25A41	SLC25A35	Q3KQZ1	498
SLC25A41	PRR22	Q8IZ63	478
SLC25A41	SMIM8	Q96KF7	451
SLC25A41	CTIF	O43310	419
SLC25A41	TDRD6	O60522	392
SLC25A41	TOMM20L	Q6UXN7	383
SLC25A41	SRP68	Q9UHB9	357
SLC25A41	F6RGN5	F6RGN5	352
SLC25A41	CBY2	Q8NA61	334
SLC25A41	DPM3	Q9P2X0	332
SLC25A41	TMEM98	Q9Y2Y6	332
SLC25A41	DENND1C	Q8IV53	330
SLC25A41	SLC25A52	Q3SY17	328

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SLC25A41	NUDT19	psi-mi:“MI:0914”(association)	0.530
SLC25A41	VPS37C	psi-mi:“MI:0914”(association)	0.350
SLC25A41	TMOD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (196): HSPD1 (Affinity Capture-MS), AP2M1 (Affinity Capture-MS), SPECC1L (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), PALM (Affinity Capture-MS), RP2 (Affinity Capture-MS), STXBP2 (Affinity Capture-MS), BMP2K (Affinity Capture-MS), EPS15 (Affinity Capture-MS), RALBP1 (Affinity Capture-MS), MFAP1 (Affinity Capture-MS), MPP7 (Affinity Capture-MS), RPRD1B (Affinity Capture-MS), TMOD2 (Affinity Capture-MS), AP2A1 (Affinity Capture-MS)

ESM2 similar proteins: A2A3V2, A3LVX1, A5DIS9, A5DX39, A6ZV78, A7A285, A7TDX5, B0G159, B3LUQ6, B4F8I5, B5VI70, F4HW79, F4JU70, K7VYZ9, O13660, O94344, O94370, P15798, P39953, P40464, P40556, P43617, P53257, Q0II44, Q19529, Q20799, Q27151, Q3MHI3, Q54VX4, Q5H9E4, Q5U3V7, Q628Z2, Q6C107, Q6CQR3, Q6DHS9, Q6FTE5, Q6ZT89, Q75EP3, Q84UC7, Q86I81

Diamond homologs: A0JN87, A1DI57, A2A3V2, A2CEQ0, A5PJZ1, B8ZHC9, F1R4U0, G3Y1Q5, O04619, O18757, O60029, O97470, P16260, P16261, P29518, P32089, P53007, P79110, Q01356, Q01888, Q08DK7, Q0CEN9, Q0II44, Q0V7M4, Q10248, Q12251, Q12482, Q2UCW8, Q3SZK0, Q4X022, Q54MZ4, Q5HZE0, Q5RFB7, Q5U3V7, Q5XHA0, Q6NYZ6, Q6PGY3, Q7T0U6, Q7ZY36, Q8BMD8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	79
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

734 predictions. Top by Δscore:

Variant	Effect	Δscore
19:6427115:T:TA	donor_gain	1.0000
19:6427328:CCATA:C	donor_loss	1.0000
19:6427329:CATA:C	donor_loss	1.0000
19:6427331:TACC:T	donor_loss	1.0000
19:6427332:A:AC	donor_gain	1.0000
19:6427333:C:CC	donor_gain	1.0000
19:6427333:CCT:C	donor_gain	1.0000
19:6427499:CAC:C	acceptor_gain	1.0000
19:6427501:CCTG:C	acceptor_loss	1.0000
19:6427502:C:CC	acceptor_gain	1.0000
19:6427502:C:CG	acceptor_loss	1.0000
19:6427503:T:C	acceptor_loss	1.0000
19:6427508:A:AC	acceptor_gain	1.0000
19:6427508:A:C	acceptor_gain	1.0000
19:6427512:C:CT	acceptor_gain	1.0000
19:6427513:G:T	acceptor_gain	1.0000
19:6429718:TCTTA:T	donor_loss	1.0000
19:6429720:TTA:T	donor_loss	1.0000
19:6429721:T:TA	donor_loss	1.0000
19:6429827:TTGCA:T	acceptor_gain	1.0000
19:6429828:TGCA:T	acceptor_gain	1.0000
19:6429829:GCA:G	acceptor_gain	1.0000
19:6429830:CA:C	acceptor_gain	1.0000
19:6429830:CAC:C	acceptor_gain	1.0000
19:6429832:C:CC	acceptor_gain	1.0000
19:6430038:A:AC	donor_gain	1.0000
19:6430039:C:CC	donor_gain	1.0000
19:6430042:AGGAG:A	donor_gain	1.0000
19:6430043:G:C	donor_gain	1.0000
19:6426562:C:CC	acceptor_gain	0.9900

AlphaMissense

2375 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:6430046:G:T	A160D	0.992
19:6430024:G:C	F167L	0.991
19:6430024:G:T	F167L	0.991
19:6430026:A:G	F167L	0.991
19:6430034:G:T	A164D	0.986
19:6427493:C:A	K211N	0.985
19:6427493:C:G	K211N	0.985
19:6430043:G:T	P161H	0.985
19:6427143:G:C	S300R	0.984
19:6427143:G:T	S300R	0.984
19:6427145:T:G	S300R	0.984
19:6427396:C:G	G244R	0.984
19:6427156:C:T	G296D	0.982
19:6430069:G:C	N152K	0.982
19:6430069:G:T	N152K	0.982
19:6429761:G:T	A196D	0.981
19:6430051:C:A	K158N	0.981
19:6430051:C:G	K158N	0.981
19:6426455:C:A	K349N	0.980
19:6426455:C:G	K349N	0.980
19:6427123:C:G	R307P	0.980
19:6430080:A:G	W149R	0.979
19:6430080:A:T	W149R	0.979
19:6430027:C:A	K166N	0.977
19:6430027:C:G	K166N	0.977
19:6430035:C:G	A164P	0.976
19:6432092:C:G	R107P	0.976
19:6427160:A:G	C295R	0.975
19:6430074:C:G	G151R	0.975
19:6427395:C:T	G244D	0.974

dbSNP variants (sampled 300 via entrez): RS1000362447 (19:6425573 C>A,G), RS1000422722 (19:6432000 C>T), RS1000444622 (19:6436756 C>T), RS1000699920 (19:6436442 G>T), RS1000758584 (19:6431398 G>A), RS1000800364 (19:6425743 C>A,T), RS1000932963 (19:6435966 A>G), RS1001110991 (19:6425729 C>A,T), RS1001330994 (19:6428144 C>A,T), RS1001858023 (19:6428220 C>A,T), RS1001888150 (19:6434574 A>G), RS1001940309 (19:6434851 G>C), RS1002336929 (19:6437902 T>TA), RS1002381580 (19:6426897 C>G), RS1002490017 (19:6434479 C>G)

Disease associations

OMIM: gene MIM:610822 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

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 — Mitochondrial nucleotide transporter subfamily

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, decreases expression	2
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	increases expression	1
Cadmium	decreases expression, increases abundance	1
Plant Extracts	affects cotreatment, decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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