SLC25A53

Summary

SLC25A53 (solute carrier family 25 member 53, HGNC:31894) is a protein-coding gene on chromosome Xq22.2, encoding Solute carrier family 25 member 53 (Q5H9E4).

Predicted to enable NAD transmembrane transporter activity. Predicted to be involved in NAD transmembrane transport. Located in mitochondrion.

Source: NCBI Gene 401612 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_001012755

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31894
Approved symbol	SLC25A53
Name	solute carrier family 25 member 53
Location	Xq22.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000269743
Ensembl biotype	protein_coding
OMIM	300941
Entrez	401612

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000467290, ENST00000594199, ENST00000905741, ENST00000905742, ENST00000905743, ENST00000926422, ENST00000926423, ENST00000926424, ENST00000926425, ENST00000926426, ENST00000944286

RefSeq mRNA: 1 — MANE Select: NM_001012755 NM_001012755

CCDS: CCDS35363

Canonical transcript exons

ENST00000594199 — 2 exons

Exon	Start	End
ENSE00002979089	104099214	104105288
ENSE00003190858	104156878	104157009

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 87.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.5176 / max 114.8289, expressed in 1775 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200032	7.1088	1765
200031	0.9823	543
200030	0.4265	228

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	87.67	gold quality
islet of Langerhans	UBERON:0000006	84.17	gold quality
monocyte	CL:0000576	82.71	gold quality
leukocyte	CL:0000738	82.42	gold quality
smooth muscle tissue	UBERON:0001135	81.19	gold quality
sural nerve	UBERON:0015488	80.47	gold quality
rectum	UBERON:0001052	79.85	gold quality
vermiform appendix	UBERON:0001154	78.68	gold quality
colonic epithelium	UBERON:0000397	78.66	gold quality
gall bladder	UBERON:0002110	78.50	gold quality
popliteal artery	UBERON:0002250	78.05	gold quality
tibial artery	UBERON:0007610	78.00	gold quality
pancreas	UBERON:0001264	77.49	gold quality
aorta	UBERON:0000947	76.88	gold quality
right coronary artery	UBERON:0001625	76.78	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.63	gold quality
left coronary artery	UBERON:0001626	76.49	gold quality
granulocyte	CL:0000094	76.38	gold quality
stromal cell of endometrium	CL:0002255	76.31	gold quality
descending thoracic aorta	UBERON:0002345	76.24	gold quality
adrenal tissue	UBERON:0018303	76.00	gold quality
thoracic aorta	UBERON:0001515	75.84	gold quality
ascending aorta	UBERON:0001496	75.72	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.51	gold quality
body of pancreas	UBERON:0001150	75.49	gold quality
lymph node	UBERON:0000029	75.17	gold quality
muscle of leg	UBERON:0001383	74.90	gold quality
mucosa of transverse colon	UBERON:0004991	74.65	gold quality
coronary artery	UBERON:0001621	74.56	gold quality
left adrenal gland	UBERON:0001234	74.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

219 targeting SLC25A53, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3065-5P	99.97	71.56	3281

Literature-anchored findings (GeneRIF, showing 1)

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

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slc25a53	ENSMUSG00000044348
rattus_norvegicus	Slc25a53	ENSRNOG00000069699

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

Solute carrier family 25 member 53 — Q5H9E4 (reviewed: Q5H9E4)

Alternative names: Mitochondrial carrier triple repeat protein 6

All UniProt accessions (1): Q5H9E4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion inner membrane.

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

RefSeq proteins (1): NP_001012773* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00153

UniProt features (12 total): transmembrane region 6, repeat 3, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H9E4-F1	85.77	0.57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 165 (showing top): MORI_IMMATURE_B_LYMPHOCYTE_UP, GOBP_NUCLEOTIDE_TRANSPORT, GOLDRATH_ANTIGEN_RESPONSE, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOMF_NUCLEOBASE_CONTAINING_COMPOUND_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOBP_NUCLEOTIDE_TRANSMEMBRANE_TRANSPORT, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_PURINE_NUCLEOTIDE_TRANSPORT, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_ORGANELLE_INNER_MEMBRANE, GAVIN_FOXP3_TARGETS_CLUSTER_P6, MATSUDA_NATURAL_KILLER_DIFFERENTIATION, GOMF_ORGANOPHOSPHATE_ESTER_TRANSMEMBRANE_TRANSPORTER_ACTIVITY

GO Biological Process (1): NAD transmembrane transport (GO:0035352)

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

Protein interactions and networks

STRING

266 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC25A53	SLC25A43	Q8WUT9	677
SLC25A53	SLC25A35	Q3KQZ1	614
SLC25A53	SLC25A32	Q9H2D1	605
SLC25A53	SLC25A36	Q96CQ1	567
SLC25A53	SLC25A33	Q9BSK2	540
SLC25A53	SLC25A17	O43808	530
SLC25A53	METTL22	Q9BUU2	523
SLC25A53	SLC25A1	P53007	489
SLC25A53	SLC25A34	Q6PIV7	486
SLC25A53	SLC25A47	Q6Q0C1	478
SLC25A53	CCDC160	A6NGH7	467
SLC25A53	MTCH1	Q9NZJ7	456
SLC25A53	SLC25A2	Q9BXI2	451
SLC25A53	SLC25A30	Q5SVS4	451
SLC25A53	FAM174C	Q9BVV8	449

IntAct

4 interactions, top by confidence:

A	B	Type	Score
FAM136A	RBFOX3	psi-mi:“MI:0914”(association)	0.640
FAM136A	PIK3C2A	psi-mi:“MI:0914”(association)	0.530

BioGRID (5): SLC25A53 (Affinity Capture-MS), SLC25A53 (Affinity Capture-MS), SLC25A53 (Affinity Capture-MS), SLC25A53 (Cross-Linking-MS (XL-MS)), SLC25A53 (Cross-Linking-MS (XL-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: A0A0G2K5L2, A0A3G9HRV8, A1CIF6, A1CWA4, A2Q9F0, A3M019, A4RPU0, A5D9W9, A6RAY2, A6S8E0, A6ZXL1, A7F9Y3, A7TIQ0, B0DK57, B0Y4J4, B2MVX9, B2VSU4, B3LH09, F4JU70, O13844, P0CAT2, Q05AQ3, Q07534, Q08CI8, Q0CT66, Q1DRJ3, Q2H608, Q2UU67, Q499U1, Q4PDL5, Q4WQC5, Q54DU1, Q54QI8, Q59KC4, Q5B717, Q5EAC0, Q5H9E4, Q5PQM9, Q6BH02, Q6C6I3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	77
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1310 predictions. Top by Δscore:

Variant	Effect	Δscore
X:104105192:T:A	donor_gain	1.0000
X:104156874:AAACC:A	donor_loss	1.0000
X:104156875:AACCT:A	donor_loss	1.0000
X:104156876:ACC:A	donor_loss	1.0000
X:104156877:C:CA	donor_loss	1.0000
X:104156879:T:TA	donor_gain	1.0000
X:104156920:T:A	donor_gain	1.0000
X:104112802:G:GG	donor_gain	0.9900
X:104112978:GATT:G	donor_gain	0.9900
X:104113426:C:CA	acceptor_gain	0.9900
X:104131087:T:TA	donor_gain	0.9900
X:104131137:G:C	donor_gain	0.9900
X:104156877:CCT:C	donor_gain	0.9900
X:104105167:AGG:A	donor_gain	0.9800
X:104112938:G:GT	donor_gain	0.9800
X:104113427:G:A	acceptor_gain	0.9800
X:104113432:A:AG	acceptor_gain	0.9800
X:104113433:G:GG	acceptor_gain	0.9800
X:104131088:C:A	donor_gain	0.9800
X:104156876:A:AC	donor_gain	0.9800
X:104156877:C:CC	donor_gain	0.9800
X:104113424:C:CA	acceptor_gain	0.9700
X:104156876:ACCT:A	donor_gain	0.9700
X:104156877:CCTC:C	donor_gain	0.9700
X:104104369:T:TA	donor_gain	0.9600
X:104105289:C:CC	acceptor_gain	0.9600
X:104112808:A:T	donor_gain	0.9600
X:104112997:TTAAG:T	donor_loss	0.9600
X:104112998:TAAG:T	donor_loss	0.9600
X:104112999:AAG:A	donor_loss	0.9600

AlphaMissense

1981 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:104104601:A:C	S219R	0.995
X:104104601:A:T	S219R	0.995
X:104104603:T:G	S219R	0.995
X:104104970:A:C	F96L	0.995
X:104104970:A:T	F96L	0.995
X:104104972:A:G	F96L	0.995
X:104105120:A:C	F46L	0.994
X:104105120:A:T	F46L	0.994
X:104105122:A:G	F46L	0.994
X:104104679:A:C	F193L	0.993
X:104104679:A:T	F193L	0.993
X:104104681:A:G	F193L	0.993
X:104104873:C:G	A129P	0.993
X:104105099:G:C	F53L	0.993
X:104105099:G:T	F53L	0.993
X:104105101:A:G	F53L	0.993
X:104104700:G:C	S186R	0.992
X:104104700:G:T	S186R	0.992
X:104104702:T:G	S186R	0.992
X:104105108:C:A	K50N	0.991
X:104105108:C:G	K50N	0.991
X:104104408:A:G	W284R	0.990
X:104104408:A:T	W284R	0.990
X:104104896:C:T	G121E	0.990
X:104104897:C:A	G121W	0.990
X:104104670:C:A	K196N	0.989
X:104104670:C:G	K196N	0.989
X:104104691:A:C	S189R	0.989
X:104104691:A:T	S189R	0.989
X:104104693:T:G	S189R	0.989

dbSNP variants (sampled 300 via entrez): RS1000501928 (X:104130734 A>G), RS1000582685 (X:104120809 A>T), RS1000650704 (X:104123502 G>A,T), RS1000950787 (X:104152109 G>A), RS1001018946 (X:104140154 A>T), RS1001201892 (X:104123399 C>T), RS1001448355 (X:104140582 C>A,T), RS1001653187 (X:104131420 G>A), RS1001684511 (X:104132000 A>G), RS1001846687 (X:104139430 T>C), RS1001917992 (X:104141684 C>T), RS1001995265 (X:104129391 A>G), RS1002087346 (X:104120224 A>G), RS1002152086 (X:104122915 G>A), RS1002426559 (X:104129839 C>T)

Disease associations

OMIM: gene MIM:300941 | 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 — Miscellaneous SLC25 mitochondrial transporters

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases methylation	4
mercuric bromide	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Ketoconazole	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Thiram	increases expression	1
Urethane	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4KJ	HCT116-SLC25A53-KO-c2	Cancer cell line	Male
CVCL_D4KK	HCT116-SLC25A53-KO-c30	Cancer cell line	Male

Clinical trials (associated diseases)

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