SLC25A43

Summary

SLC25A43 (solute carrier family 25 member 43, HGNC:30557) is a protein-coding gene on chromosome Xq24, encoding Solute carrier family 25 member 43 (Q8WUT9).

This gene encodes a member of the mitochondrial carrier family of proteins.

Source: NCBI Gene 203427 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 81 total — 1 likely-pathogenic
• MANE Select transcript: NM_145305

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30557
Approved symbol	SLC25A43
Name	solute carrier family 25 member 43
Location	Xq24
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000077713
Ensembl biotype	protein_coding
OMIM	300641
Entrez	203427

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000217909, ENST00000484058, ENST00000488158, ENST00000493093, ENST00000892970

RefSeq mRNA: 1 — MANE Select: NM_145305 NM_145305

CCDS: CCDS14577

Canonical transcript exons

ENST00000217909 — 5 exons

Exon	Start	End
ENSE00001681987	119399336	119399678
ENSE00001731111	119452865	119454478
ENSE00003487721	119406460	119406701
ENSE00003584104	119452009	119452143
ENSE00003586266	119410190	119410362

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 91.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.9392 / max 55.0022, expressed in 1705 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197390	7.9392	1705

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
esophagus squamous epithelium	UBERON:0006920	91.77	gold quality
lower esophagus mucosa	UBERON:0035834	90.28	gold quality
jejunal mucosa	UBERON:0000399	89.56	gold quality
gingiva	UBERON:0001828	89.19	gold quality
gingival epithelium	UBERON:0001949	88.62	gold quality
esophagus mucosa	UBERON:0002469	88.62	gold quality
oral cavity	UBERON:0000167	87.45	gold quality
calcaneal tendon	UBERON:0003701	86.79	gold quality
rectum	UBERON:0001052	86.05	gold quality
skin of abdomen	UBERON:0001416	84.32	gold quality
colonic mucosa	UBERON:0000317	84.27	gold quality
mammalian vulva	UBERON:0000997	84.18	gold quality
zone of skin	UBERON:0000014	84.09	gold quality
mucosa of transverse colon	UBERON:0004991	83.93	gold quality
skin of leg	UBERON:0001511	83.84	gold quality
skin of hip	UBERON:0001554	83.83	gold quality
esophagus	UBERON:0001043	83.71	gold quality
duodenum	UBERON:0002114	83.51	gold quality
stromal cell of endometrium	CL:0002255	83.30	gold quality
mouth mucosa	UBERON:0003729	83.15	gold quality
mucosa of sigmoid colon	UBERON:0004993	82.86	gold quality
vagina	UBERON:0000996	82.85	gold quality
omental fat pad	UBERON:0010414	82.69	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.65	gold quality
peritoneum	UBERON:0002358	82.63	gold quality
minor salivary gland	UBERON:0001830	82.34	gold quality
adipose tissue of abdominal region	UBERON:0007808	82.24	gold quality
tibial nerve	UBERON:0001323	82.03	gold quality
adipose tissue	UBERON:0001013	82.02	gold quality
transverse colon	UBERON:0001157	82.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting SLC25A43, 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-6867-5P	100.00	82.21	3464
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-513A-3P	99.39	70.63	3620

Literature-anchored findings (GeneRIF, showing 5)

• associations between site-specific methylation and clinicopathological parameters suggest that epigenetic changes in SLC25A43 gene could be of importance in breast carcinogenesis. (PMID:22430806)
• Our results indicate a possible role of SLC25A43 in HER2-positive breast cancer and support the hypothesis of altered mitochondrial function in cancer. (PMID:22883974)
• Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)
• Our findings demonstrate that the mitochondrial protein SLC25A43 affects drug efficacy and cell cycle regulation following drug exposure in breast cancer cell lines. (PMID:23354756)
• In line with our previous results, we show a role for SLC25A43 as a regulator of cell cycle progression and proliferation through a putative mitochondrial checkpoint. (PMID:26721434)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc25a43	ENSDARG00000102048
mus_musculus	Slc25a43	ENSMUSG00000037636
rattus_norvegicus	Slc25a43	ENSRNOG00000012756

Paralogs (49): SLC25A13 (ENSG00000004864), SLC25A5 (ENSG00000005022), SLC25A39 (ENSG00000013306), SLC25A40 (ENSG00000075303), SLC25A3 (ENSG00000075415), 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), UCP2 (ENSG00000175567)

Protein

Protein identifiers

Solute carrier family 25 member 43 — Q8WUT9 (reviewed: Q8WUT9)

All UniProt accessions (1): Q8WUT9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion inner membrane.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WUT9-1	1	yes
Q8WUT9-2	2

RefSeq proteins (1): NP_660348* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00153

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WUT9-F1	88.76	0.64

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_TRANSMEMBRANE_TRANSPORT, SENESE_HDAC3_TARGETS_DN, NUYTTEN_EZH2_TARGETS_DN, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_ORGANELLE_ENVELOPE, chrXq24, JOHNSTONE_PARVB_TARGETS_3_DN, PECE_MAMMARY_STEM_CELL_DN, RBM34_TARGET_GENES, ZNF768_TARGET_GENES, MIR6867_5P, MIR7110_3P

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

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
organelle inner membrane	1
mitochondrial membrane	1
cytoplasm	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1045 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC25A43	SLC25A53	Q5H9E4	677
SLC25A43	STEEP1	Q9H5V9	582
SLC25A43	SEPTIN6	Q14141	471
SLC25A43	FRMD7	Q6ZUT3	456
SLC25A43	SLC25A52	Q3SY17	439
SLC25A43	SLC25A51	Q9H1U9	423
SLC25A43	F6RGN5	F6RGN5	377
SLC25A43	SLC25A10	Q9UBX3	377
SLC25A43	CFAP77	Q6ZQR2	373
SLC25A43	UBE2A	P49459	352
SLC25A43	NUP62CL	Q9H1M0	348
SLC25A43	RNF113A	O15541	347
SLC25A43	ADCK2	Q7Z695	346
SLC25A43	PRR32	B1ATL7	337
SLC25A43	KLHL15	Q96M94	336

IntAct

5 interactions, top by confidence:

A	B	Type	Score
SLC25A43	HSPD1	psi-mi:“MI:0914”(association)	0.530
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
CUL1	LGALS8	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): PROSER2 (Affinity Capture-MS), NDEL1 (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), SLC25A43 (Affinity Capture-RNA), SLC25A43 (Affinity Capture-MS), TFAP4 (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), NDEL1 (Affinity Capture-MS), PROSER2 (Affinity Capture-MS), SLC25A43 (Affinity Capture-RNA), SLC25A43 (Affinity Capture-MS), SLC25A43 (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, A2A3V2, A4RPU0, F1LZW6, G3YAF3, G3YFS7, O04200, O43772, O77792, O95258, O97649, P16260, P33303, P39953, P97521, Q03028, Q08DK7, Q12482, Q3ZBJ8, Q54FE6, Q54RB9, Q54S10, Q55GE2, Q5HZE0, Q5RFB7, Q68F18, Q6GLJ0, Q6PGY3, Q75AH6, Q7DNC3, Q86AV5, Q86I81, Q8BL03, Q8BZ09, Q8HXW2, Q8HXY2, Q8WUT9, Q93XM7, Q99297, Q99JD3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	32
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2580340	GRCh37/hg19 Xq24(chrX:118544103-118676607)x0	Likely pathogenic

SpliceAI

1200 predictions. Top by Δscore:

Variant	Effect	Δscore
X:119399679:G:GG	donor_gain	1.0000
X:119406656:G:GT	donor_gain	1.0000
X:119399675:GCAA:G	donor_gain	0.9900
X:119452864:GATA:G	acceptor_gain	0.9900
X:119452953:T:A	acceptor_gain	0.9900
X:119399676:C:T	donor_gain	0.9800
X:119399676:CAAG:C	donor_loss	0.9800
X:119399677:AAG:A	donor_loss	0.9800
X:119399678:AG:A	donor_loss	0.9800
X:119399679:G:A	donor_loss	0.9800
X:119399680:T:G	donor_loss	0.9800
X:119406619:G:GT	donor_gain	0.9800
X:119406657:A:T	donor_gain	0.9700
X:119417538:T:A	acceptor_gain	0.9700
X:119452952:CTG:C	acceptor_gain	0.9700
X:119400453:T:TA	donor_gain	0.9600
X:119400454:A:AA	donor_gain	0.9600
X:119410360:CAGG:C	donor_loss	0.9600
X:119410361:AGGTG:A	donor_loss	0.9600
X:119410362:GGTG:G	donor_loss	0.9600
X:119410363:G:GA	donor_loss	0.9600
X:119410364:T:G	donor_loss	0.9600
X:119400013:A:G	donor_gain	0.9500
X:119410185:TGCAG:T	acceptor_loss	0.9500
X:119410186:GCAGG:G	acceptor_loss	0.9500
X:119410187:CAGGT:C	acceptor_loss	0.9500
X:119410188:A:G	acceptor_loss	0.9500
X:119410189:G:GA	acceptor_loss	0.9500
X:119417537:CTGAG:C	acceptor_gain	0.9500
X:119418673:T:A	acceptor_gain	0.9500

AlphaMissense

2185 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:119399485:A:C	S28R	0.975
X:119399487:C:A	S28R	0.975
X:119399487:C:G	S28R	0.975
X:119406524:A:C	S114R	0.971
X:119406526:T:A	S114R	0.971
X:119406526:T:G	S114R	0.971
X:119399479:A:C	S26R	0.961
X:119399481:C:A	S26R	0.961
X:119399481:C:G	S26R	0.961
X:119410330:T:C	F220L	0.958
X:119410332:T:A	F220L	0.958
X:119410332:T:G	F220L	0.958
X:119410350:G:C	K226N	0.957
X:119410350:G:T	K226N	0.957
X:119452054:T:C	F246L	0.957
X:119452056:C:A	F246L	0.957
X:119452056:C:G	F246L	0.957
X:119406582:G:C	R133P	0.955
X:119452074:C:G	C252W	0.953
X:119410297:T:C	C209R	0.952
X:119399614:G:A	G71R	0.947
X:119399614:G:C	G71R	0.947
X:119410362:G:C	Q230H	0.938
X:119410362:G:T	Q230H	0.938
X:119452121:G:A	G268E	0.936
X:119410201:T:C	F177L	0.934
X:119410203:C:A	F177L	0.934
X:119410203:C:G	F177L	0.934
X:119406576:A:T	K131I	0.933
X:119399629:T:C	C76R	0.932

dbSNP variants (sampled 300 via entrez): RS1000007124 (X:119420726 A>T), RS1000019219 (X:119405958 G>A,C), RS1000038278 (X:119450581 T>G), RS1000085996 (X:119433344 T>C), RS1000127506 (X:119419413 C>T), RS1000310739 (X:119432867 T>C), RS1000356157 (X:119415300 G>A,C), RS1000625056 (X:119409372 A>G), RS1000729209 (X:119416923 G>A), RS1000832945 (X:119414761 T>C), RS1000879315 (X:119408080 G>A), RS1000908746 (X:119407604 A>C), RS1000912861 (X:119409766 A>G), RS1000914221 (X:119441562 T>C), RS1001085284 (X:119423090 C>G)

Disease associations

OMIM: gene MIM:300641 | disease phenotypes: MIM:301013

GenCC curated gene-disease

Mondo (1): intellectual disability, X-linked 107 (MONDO:0049222)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001086_4	Paget’s disease	1.000000e-07
GCST007876_61	Estimated glomerular filtration rate	5.000000e-10
GCST008839_405	Height	3.000000e-22

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

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	3
(+)-JQ1 compound	decreases expression	2
Air Pollutants	decreases expression, increases abundance	2
Tretinoin	decreases expression	2
Valproic Acid	increases expression	2
Aflatoxin B1	decreases expression, increases methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
trichostatin A	increases expression	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Acetaminophen	decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Quercetin	decreases expression	1
Sodium Dodecyl Sulfate	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Palmitic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4KB	HCT116-SLC25A43-KO-c18	Cancer cell line	Male
CVCL_D4KC	HCT116-SLC25A43-KO-c4	Cancer cell line	Male
CVCL_TM50	HAP1 SLC25A43 (-) 1	Cancer cell line	Male
CVCL_XT06	HAP1 SLC25A43 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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