SLC25A45

Summary

SLC25A45 (solute carrier family 25 member 45, HGNC:27442) is a protein-coding gene on chromosome 11q13.1, encoding Solute carrier family 25 member 45 (Q8N413).

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion.

Source: NCBI Gene 283130 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_182556

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27442
Approved symbol	SLC25A45
Name	solute carrier family 25 member 45
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000162241
Ensembl biotype	protein_coding
OMIM	610825
Entrez	283130

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 9 protein_coding, 5 nonsense_mediated_decay, 4 retained_intron

ENST00000294187, ENST00000398802, ENST00000524438, ENST00000525944, ENST00000526259, ENST00000526432, ENST00000526898, ENST00000527174, ENST00000529431, ENST00000529962, ENST00000530936, ENST00000531791, ENST00000533629, ENST00000534028, ENST00000534338, ENST00000909312, ENST00000909313, ENST00000966869

RefSeq mRNA: 9 — MANE Select: NM_182556 NM_001077241, NM_001278250, NM_001278251, NM_001300820, NM_001352381, NM_001352382, NM_001352383, NM_001352384, NM_182556

CCDS: CCDS41670, CCDS41671, CCDS60850, CCDS76431

Canonical transcript exons

ENST00000398802 — 7 exons

Exon	Start	End
ENSE00001384826	65375192	65376675
ENSE00001407422	65382486	65382646
ENSE00003481572	65381915	65381969
ENSE00003557798	65376818	65377076
ENSE00003622004	65379376	65379561
ENSE00003631582	65380132	65380175
ENSE00003668445	65379867	65379938

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 91.81.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4407 / max 58.3196, expressed in 473 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120554	1.1743	336
120553	0.2664	114

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	91.81	gold quality
granulocyte	CL:0000094	91.54	gold quality
ileal mucosa	UBERON:0000331	88.38	gold quality
right lobe of thyroid gland	UBERON:0001119	87.80	gold quality
left lobe of thyroid gland	UBERON:0001120	87.01	gold quality
thyroid gland	UBERON:0002046	86.39	gold quality
spleen	UBERON:0002106	85.99	gold quality
bone marrow cell	CL:0002092	85.37	gold quality
vermiform appendix	UBERON:0001154	84.63	gold quality
lymph node	UBERON:0000029	84.43	gold quality
pancreas	UBERON:0001264	84.05	gold quality
blood	UBERON:0000178	83.92	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.84	gold quality
tibialis anterior	UBERON:0001385	83.66	silver quality
right lobe of liver	UBERON:0001114	83.25	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.07	gold quality
apex of heart	UBERON:0002098	82.90	gold quality
muscle of leg	UBERON:0001383	82.34	gold quality
sural nerve	UBERON:0015488	82.33	gold quality
small intestine	UBERON:0002108	82.29	gold quality
gastrocnemius	UBERON:0001388	82.20	gold quality
pancreatic ductal cell	CL:0002079	81.84	silver quality
kidney epithelium	UBERON:0004819	81.20	silver quality
leukocyte	CL:0000738	81.15	gold quality
monocyte	CL:0000576	80.77	gold quality
duodenum	UBERON:0002114	80.67	gold quality
caecum	UBERON:0001153	80.09	gold quality
minor salivary gland	UBERON:0001830	79.65	gold quality
pituitary gland	UBERON:0000007	79.56	gold quality
adenohypophysis	UBERON:0002196	79.01	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.53
E-MTAB-7606	no	296.31
E-MTAB-7303	no	78.13
E-GEOD-99795	no	42.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting SLC25A45, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
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-6825-5P	99.96	69.81	3431
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-7106-5P	99.53	67.47	3574

Literature-anchored findings (GeneRIF, showing 1)

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

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000102513
mus_musculus	Slc25a45	ENSMUSG00000024818
rattus_norvegicus	Slc25a45	ENSRNOG00000030616

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), SLC25A34 (ENSG00000162461), SLC25A32 (ENSG00000164933), SLC25A6 (ENSG00000169100), SLC25A33 (ENSG00000171612), SLC25A30 (ENSG00000174032), UCP3 (ENSG00000175564), UCP2 (ENSG00000175567)

Protein

Protein identifiers

Solute carrier family 25 member 45 — Q8N413 (reviewed: Q8N413)

All UniProt accessions (6): E9PJ15, E9PJQ3, E9PJW2, E9PK53, E9PMF0, Q8N413

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion inner membrane.

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

Isoforms (4)

UniProt ID	Names	Canonical?
Q8N413-1	1	yes
Q8N413-2	2
Q8N413-3	3
Q8N413-4	4

RefSeq proteins (9): NP_001070709, NP_001265179, NP_001265180, NP_001287749, NP_001339310, NP_001339311, NP_001339312, NP_001339313, NP_872362* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002067	MCP	Family
IPR018108	MCP_transmembrane	Repeat
IPR023395	MCP_dom_sf	Homologous_superfamily
IPR050567	Mitochondrial_Carrier	Family

Pfam: PF00153

UniProt features (16 total): transmembrane region 6, splice variant 3, repeat 3, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N413-F1	80.25	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 147 (showing top): chr11q13, RGTTAMWNATT_HNF1_01, GOCC_MITOCHONDRIAL_ENVELOPE, TGANTCA_AP1_C, GOBP_TRANSMEMBRANE_TRANSPORT, AR_01, GOCC_ORGANELLE_INNER_MEMBRANE, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_TRANSPORTER_ACTIVITY, MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, GOCC_ORGANELLE_ENVELOPE, SERVITJA_LIVER_HNF1A_TARGETS_DN, GCNP_SHH_UP_LATE.V1_DN, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_IL2_CULTURE_DN

GO Biological Process (1): transmembrane transport (GO:0055085)

GO Molecular Function (1): transmembrane transporter activity (GO:0022857)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020), mitochondrial membrane (GO:0031966)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
transporter activity	1
transmembrane transport	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1
mitochondrion	1
mitochondrial envelope	1
organelle membrane	1

Protein interactions and networks

STRING

602 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC25A45	FRMD8	Q9BZ67	618
SLC25A45	FAM89B	Q8N5H3	614
SLC25A45	TIGD3	Q6B0B8	613
SLC25A45	ANKRD22	Q5VYY1	571
SLC25A45	CDC42EP2	O14613	534
SLC25A45	MCOLN3	Q8TDD5	509
SLC25A45	ZNRD2	O60232	497
SLC25A45	EHBP1L1	Q8N3D4	476
SLC25A45	BMAL2	Q8WYA1	469
SLC25A45	SLC5A9	Q2M3M2	452
SLC25A45	SLC16A13	Q7RTY0	449
SLC25A45	KLK10	O43240	439
SLC25A45	KCNK7	Q9Y2U2	436
SLC25A45	SLC25A52	Q3SY17	432
SLC25A45	TPK1	Q9H3S4	430

IntAct

0 interactions, top by confidence:

BioGRID (2): SLC25A45 (Positive Genetic), SLC25A45 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0U2IR85, A0A3G9HRV8, A0PC02, A5DIS9, F4HW79, G3YFS7, K3VFR5, O14281, O81845, O94370, P23500, P25874, P32331, P32332, P38087, P38152, P38921, P40035, Q03028, Q06143, Q10248, Q12375, Q18P97, Q1ECW7, Q3MHI3, Q54B67, Q54BM3, Q54FE6, Q54W11, Q55DY8, Q55GE2, Q6C107, Q6CQR3, Q6DHS9, Q6FTN2, Q6ZT89, Q7DNC3, Q84UC7, Q8BW66, Q8CFJ7

Diamond homologs: A0A0G2K309, F4HW79, O04200, O22261, O43772, O94502, P10566, P32331, P38087, P39953, P40556, P97521, Q06143, Q08DK7, Q12289, Q12375, Q27257, Q3ZBJ8, Q54BM3, Q54FE6, Q54W11, Q5HZE0, Q5XGI1, Q68F18, Q6BPW0, Q6GLJ0, Q6GQ22, Q76P23, Q84UC7, Q8BL03, Q8BW66, Q8CFJ7, Q8HXY2, Q8N413, Q8N8R3, Q8RXZ9, Q93XM7, Q9BXI2, Q9CA93, Q9UTD6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1274 predictions. Top by Δscore:

Variant	Effect	Δscore
11:65376812:A:AC	donor_gain	1.0000
11:65376813:C:CC	donor_gain	1.0000
11:65376813:CTTA:C	donor_gain	1.0000
11:65376814:TTA:T	donor_loss	1.0000
11:65376816:A:AC	donor_gain	1.0000
11:65376817:C:CA	donor_gain	1.0000
11:65376817:CT:C	donor_gain	1.0000
11:65376817:CTG:C	donor_gain	1.0000
11:65376817:CTGG:C	donor_gain	1.0000
11:65376817:CTGGG:C	donor_gain	1.0000
11:65377055:C:CT	acceptor_gain	1.0000
11:65379421:G:C	donor_gain	1.0000
11:65379865:A:AC	donor_gain	1.0000
11:65379866:C:CC	donor_gain	1.0000
11:65379866:CGGA:C	donor_gain	1.0000
11:65379937:ACC:A	acceptor_loss	1.0000
11:65379938:CCT:C	acceptor_loss	1.0000
11:65376671:TGAGC:T	acceptor_gain	0.9900
11:65376672:GAGCC:G	acceptor_gain	0.9900
11:65376673:AGCCT:A	acceptor_gain	0.9900
11:65376674:GC:G	acceptor_gain	0.9900
11:65376674:GCCT:G	acceptor_gain	0.9900
11:65376675:CC:C	acceptor_gain	0.9900
11:65376676:C:CC	acceptor_gain	0.9900
11:65376682:C:CT	acceptor_gain	0.9900
11:65376683:A:T	acceptor_gain	0.9900
11:65377075:GCC:G	acceptor_loss	0.9900
11:65377077:C:CA	acceptor_loss	0.9900
11:65377078:T:A	acceptor_loss	0.9900
11:65379370:CCTCA:C	donor_loss	0.9900

AlphaMissense

1854 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:65379493:A:C	F74L	0.992
11:65379493:A:T	F74L	0.992
11:65379495:A:G	F74L	0.992
11:65377044:T:A	K124N	0.991
11:65377044:T:G	K124N	0.991
11:65377045:T:A	K124I	0.991
11:65376596:C:A	K226N	0.989
11:65376596:C:G	K226N	0.989
11:65377032:T:A	Q128H	0.989
11:65377032:T:G	Q128H	0.989
11:65379520:G:C	S65R	0.989
11:65379520:G:T	S65R	0.989
11:65379522:T:G	S65R	0.989
11:65379543:C:G	G58R	0.989
11:65379543:C:T	G58R	0.989
11:65376437:G:C	S279R	0.987
11:65376437:G:T	S279R	0.987
11:65376439:T:G	S279R	0.987
11:65380132:C:A	K27N	0.987
11:65380132:C:G	K27N	0.987
11:65376453:G:T	A274D	0.985
11:65379894:G:C	C42W	0.983
11:65376454:C:G	A274P	0.982
11:65376476:A:C	S266R	0.982
11:65376476:A:T	S266R	0.982
11:65376478:T:G	S266R	0.982
11:65380175:C:T	G13D	0.982
11:65376443:G:C	F277L	0.981
11:65376443:G:T	F277L	0.981
11:65376445:A:G	F277L	0.981

dbSNP variants (sampled 300 via entrez): RS1000078572 (11:65378634 G>T), RS1000584157 (11:65374717 C>T), RS1000820805 (11:65377755 T>A), RS1000869584 (11:65383411 G>A,C,T), RS1000885325 (11:65378852 C>T), RS1000941399 (11:65383123 G>A), RS1001075368 (11:65379940 T>A,G), RS1001757729 (11:65379415 C>A,T), RS1002224366 (11:65384219 C>T), RS1002358874 (11:65380940 A>G), RS1002370838 (11:65375220 G>A), RS1002995525 (11:65380656 C>G,T), RS1003430312 (11:65385636 A>G), RS1003462027 (11:65385214 C>G), RS1003761008 (11:65382208 C>T)

Disease associations

OMIM: gene MIM:610825 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST002239_27	Symmetrical dimethylarginine levels	2.000000e-10
GCST002481_8	Acne (severe)	3.000000e-11
GCST007877_14	Creatinine levels	3.000000e-08
GCST010002_240	Refractive error	3.000000e-11
GCST012020_185	Serum metabolite levels	1.000000e-13
GCST012021_110	Serum metabolite levels	1.000000e-13

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 amino acid transporter subfamily

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	affects expression, increases expression	3
Acetaminophen	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases methylation	1
mono-(2-ethylhexyl)phthalate	increases abundance, decreases methylation	1
sulindac sulfide	increases expression	1
ferrous chloride	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	increases expression, affects cotreatment	1
Diethylhexyl Phthalate	decreases methylation, increases abundance	1
Ethinyl Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Folic Acid	decreases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Silicon Dioxide	increases expression	1
Smoke	increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4SQ	HuH7-SLC25A45-KO-c3	Cancer cell line	Male
CVCL_D4SR	HuH7-SLC25A45-KO-c6	Cancer cell line	Male
CVCL_TM52	HAP1 SLC25A45 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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