SLC25A52

Summary

SLC25A52 (solute carrier family 25 member 52, HGNC:23324) is a protein-coding gene on chromosome 18q12.1, encoding Mitochondrial nicotinamide adenine dinucleotide transporter SLC25A52 (Q3SY17). Mitochondrial membrane carrier protein that mediates the import of NAD(+) into mitochondria.

This gene is similar to the mitochondrial carrier triple repeat 1 gene on chromosome 9. The gene is intronless and may be an evolving pseudogene; however, it is transcribed and it contains a full-length coding region so it is currently classified as a protein-coding locus.

Source: NCBI Gene 147407 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001034172

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23324
Approved symbol	SLC25A52
Name	solute carrier family 25 member 52
Location	18q12.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000141437
Ensembl biotype	protein_coding
OMIM	616153
Entrez	147407

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000269205, ENST00000672005

RefSeq mRNA: 1 — MANE Select: NM_001034172 NM_001034172

CCDS: CCDS32812

Canonical transcript exons

ENST00000269205 — 1 exons

Exon	Start	End
ENSE00001373615	31759584	31760880

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 84.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0269 / max 13.0815, expressed in 6 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
171592	0.0269	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.70	gold quality
testis	UBERON:0000473	69.07	gold quality
left testis	UBERON:0004533	68.71	gold quality
right testis	UBERON:0004534	67.91	gold quality
stromal cell of endometrium	CL:0002255	57.51	gold quality
cortical plate	UBERON:0005343	56.10	gold quality
skeletal muscle tissue	UBERON:0001134	55.77	gold quality
liver	UBERON:0002107	55.60	gold quality
right lobe of liver	UBERON:0001114	54.48	gold quality
islet of Langerhans	UBERON:0000006	53.66	gold quality
muscle tissue	UBERON:0002385	50.24	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	50.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	48.30	gold quality
bone marrow cell	CL:0002092	47.88	gold quality
granulocyte	CL:0000094	47.57	silver quality
right adrenal gland cortex	UBERON:0035827	46.64	gold quality
colonic epithelium	UBERON:0000397	46.56	gold quality
right adrenal gland	UBERON:0001233	46.16	gold quality
endometrium	UBERON:0001295	46.15	silver quality
ganglionic eminence	UBERON:0004023	44.27	gold quality
pituitary gland	UBERON:0000007	43.97	gold quality
left adrenal gland cortex	UBERON:0035825	43.56	silver quality
left adrenal gland	UBERON:0001234	43.42	gold quality
muscle of leg	UBERON:0001383	43.24	gold quality
adenohypophysis	UBERON:0002196	43.23	gold quality
adrenal gland	UBERON:0002369	43.17	gold quality
tonsil	UBERON:0002372	42.92	silver quality
adrenal tissue	UBERON:0018303	42.47	silver quality
gastrocnemius	UBERON:0001388	42.20	gold quality
mucosa of transverse colon	UBERON:0004991	41.84	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.45

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slc25a51	ENSMUSG00000045973
rattus_norvegicus	Slc25a52	ENSRNOG00000033251
rattus_norvegicus	Slc25a51	ENSRNOG00000039278
rattus_norvegicus	Slc25a51l1	ENSRNOG00000070747

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), 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), UCP2 (ENSG00000175567)

Protein

Protein identifiers

Mitochondrial nicotinamide adenine dinucleotide transporter SLC25A52 — Q3SY17 (reviewed: Q3SY17)

Alternative names: Mitochondrial NAD(+) transporter SLC25A52, Mitochondrial carrier triple repeat protein 2, Solute carrier family 25 member 52

All UniProt accessions (2): Q3SY17, I3L0B8

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial membrane carrier protein that mediates the import of NAD(+) into mitochondria. Compared to SLC25A51, SLC25A52-mediated transport is not essential for the import of NAD(+) in mitochondria. The transport mechanism, uniport or antiport, its electrogenicity and substrate selectivity, remain to be elucidated.

Subcellular location. Mitochondrion inner membrane.

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

RefSeq proteins (1): NP_001029344* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018108	MCP_transmembrane	Repeat
IPR023395	MCP_dom_sf	Homologous_superfamily
IPR052465	Mito_NAD+_Carrier	Family

Pfam: PF00153

Catalyzed reactions (Rhea), 1 shown:

• NAD(+)(in) = NAD(+)(out) (RHEA:65408)

UniProt features (11 total): transmembrane region 6, repeat 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3SY17-F1	80.98	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): GOBP_NUCLEOTIDE_TRANSPORT, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, chr18q12, GOMF_NUCLEOBASE_CONTAINING_COMPOUND_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOBP_NUCLEOTIDE_TRANSMEMBRANE_TRANSPORT, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_PURINE_NUCLEOTIDE_TRANSPORT, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_ORGANELLE_INNER_MEMBRANE, GOMF_ORGANOPHOSPHATE_ESTER_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_NUCLEOTIDE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, GOCC_ORGANELLE_ENVELOPE, GOBP_PURINE_CONTAINING_COMPOUND_TRANSMEMBRANE_TRANSPORT

GO Biological Process (1): mitochondrial NAD transmembrane transport (GO:1990549)

GO Molecular Function (1): NAD transmembrane transporter activity (GO:0051724)

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
NAD transmembrane transport	2
adenine nucleotide transmembrane transporter activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

278 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC25A52	SLC25A32	Q9H2D1	632
SLC25A52	SLC25A33	Q9BSK2	568
SLC25A52	SLC35G4	P0C7Q5	518
SLC25A52	SLC25A48	Q6ZT89	494
SLC25A52	MTCH1	Q9NZJ7	458
SLC25A52	SLC25A47	Q6Q0C1	451
SLC25A52	SLC35G3	Q8N808	448
SLC25A52	TEX261	Q6UWH6	447
SLC25A52	SLC25A43	Q8WUT9	439
SLC25A52	SLC25A17	O43808	438
SLC25A52	SLC25A45	Q8N413	432
SLC25A52	SLC25A35	Q3KQZ1	432
SLC25A52	CXorf58	Q96LI9	419
SLC25A52	SLC25A34	Q6PIV7	413
SLC25A52	SLC25A26	Q70HW3	410

IntAct

8 interactions, top by confidence:

A	B	Type	Score
BTNL3	FAM171A2	psi-mi:“MI:0914”(association)	0.530
SLC25A52	GAPDHS	psi-mi:“MI:0915”(physical association)	0.400
	NBAS	psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350
TSPAN15	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC18A2	UBXN8	psi-mi:“MI:0914”(association)	0.350
TSPAN8	TP53I11	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): SLC25A52 (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), SLC25A52 (Affinity Capture-MS), SLC25A52 (Protein-peptide)

ESM2 similar proteins: A1CIF6, A1CWA4, A2Q9F0, A3M019, A4RPU0, A5D9W9, A6RAY2, A6S8E0, A6SL61, A6ZXL1, A7F9Y3, A7TIQ0, B0DK57, B0Y4J4, B2MVX9, B2VSU4, B3LH09, P0CAT2, P38152, P38921, Q03829, Q07534, Q08CI8, Q0CT66, Q12289, Q1DRJ3, Q2H608, Q2UU67, Q3SY17, Q4WQC5, Q52KK3, Q59KC4, Q5B717, Q5EAC0, Q5HZI9, Q6BH02, Q6C6I3, Q6CNY8, Q6DE75, Q6DJ08

Diamond homologs: Q3SY17, Q52KK3, Q55GE2, Q5H9E4, Q5HZI9, Q9H1U9, A0JN87, F1LX07, F1LZW6, G3YAF3, G3YFS7, O43772, O65023, O75746, O77792, O97470, O97649, P12236, P31692, P32007, P33303, P55851, P56500, P70406, P97521, Q03028, Q08DK7, Q10248, Q12482, Q3SZI5, Q505J6, Q54B67, Q54RB9, Q5R5A1, Q5R5A8, Q5RBC8, Q5RFB7, Q75AH6, Q76P23, Q86AV5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

255 predictions. Top by Δscore:

Variant	Effect	Δscore
18:31760062:ATGCT:A	donor_gain	0.7000
18:31760137:G:A	donor_gain	0.6800
18:31760088:C:CT	acceptor_gain	0.6700
18:31760115:T:TA	donor_gain	0.6600
18:31760066:T:A	donor_gain	0.6300
18:31760088:C:T	acceptor_gain	0.6300
18:31760117:C:CT	acceptor_gain	0.6200
18:31760110:T:TA	donor_gain	0.6100
18:31760137:G:C	donor_gain	0.6000
18:31760174:G:A	donor_gain	0.6000
18:31760136:AG:A	donor_gain	0.5900
18:31760145:A:AC	donor_gain	0.5600
18:31760100:CATTG:C	donor_gain	0.5500
18:31760081:C:A	acceptor_gain	0.5400
18:31760152:T:TA	donor_gain	0.5400
18:31760158:T:TA	donor_gain	0.5400
18:31760067:C:CA	donor_gain	0.5300
18:31760135:AAG:A	donor_gain	0.5300
18:31760009:C:A	donor_gain	0.5100
18:31760076:G:GT	donor_gain	0.5100
18:31760084:AGG:A	donor_gain	0.5000
18:31760101:A:C	donor_gain	0.4900
18:31760108:AGT:A	donor_gain	0.4900
18:31760356:A:C	acceptor_gain	0.4900
18:31760035:A:C	donor_gain	0.4800
18:31760074:G:GC	donor_gain	0.4800
18:31759808:ATG:A	donor_gain	0.4700
18:31759935:T:C	donor_gain	0.4700
18:31760073:TGGG:T	donor_gain	0.4700
18:31760246:T:TA	donor_gain	0.4700

AlphaMissense

1938 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:31760365:A:C	F99L	0.992
18:31760365:A:T	F99L	0.992
18:31760367:A:G	F99L	0.992
18:31759815:A:G	W283R	0.991
18:31759815:A:T	W283R	0.991
18:31759812:C:G	G284R	0.982
18:31760242:T:A	R140S	0.982
18:31760242:T:G	R140S	0.982
18:31759813:C:A	W283C	0.981
18:31759813:C:G	W283C	0.981
18:31760092:A:C	F190L	0.981
18:31760092:A:T	F190L	0.981
18:31760094:A:G	F190L	0.981
18:31760228:A:G	L145P	0.979
18:31759811:C:T	G284D	0.978
18:31759829:C:G	R278P	0.978
18:31760488:T:A	Q58H	0.978
18:31760488:T:G	Q58H	0.978
18:31760415:C:G	G83R	0.976
18:31760415:C:T	G83R	0.976
18:31760006:C:T	G219D	0.974
18:31759800:C:G	A288P	0.973
18:31759851:C:G	G271R	0.973
18:31759801:A:C	N287K	0.972
18:31759801:A:T	N287K	0.972
18:31759880:C:G	R261P	0.972
18:31760492:C:G	R57P	0.972
18:31760543:G:T	A40E	0.972
18:31760141:C:G	R174P	0.971
18:31760117:C:G	R182P	0.970

dbSNP variants (sampled 300 via entrez): RS1002214733 (18:31759561 C>A,G), RS1004932207 (18:31760863 G>A,C), RS1006442289 (18:31761084 A>G), RS1006848866 (18:31759318 G>A), RS1010909906 (18:31760291 G>A,T), RS1010983277 (18:31759813 C>T), RS1011203573 (18:31761185 T>C), RS1011593500 (18:31761443 C>G), RS1011811776 (18:31759373 C>T), RS1013892466 (18:31761956 G>C), RS1014639718 (18:31761863 C>T), RS1016644973 (18:31762356 A>C), RS1017045919 (18:31760648 T>C), RS1018653127 (18:31759331 A>T), RS1019048331 (18:31760869 C>T)

Disease associations

OMIM: gene MIM:616153 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002097_26	Coronary artery calcification	1.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification

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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Atrazine	increases expression	1
Cadmium	increases abundance, increases expression	1
Urethane	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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