SLC25A16

gene
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Also known as GDAD10S105EHGT.1ML7

Summary

SLC25A16 (solute carrier family 25 member 16, HGNC:10986) is a protein-coding gene on chromosome 10q21.3, encoding Mitochondrial coenzyme A transporter SLC25A16 (P16260). Mitochondrial inner membrane transporter that regulates coenzyme A homeostasis between cytosol and mitochondria.

This gene encodes a protein that contains three tandemly repeated mitochondrial carrier protein domains. The encoded protein is localized in the inner membrane and facilitates the rapid transport and exchange of molecules between the cytosol and the mitochondrial matrix space. This gene has a possible role in Graves’ disease.

Source: NCBI Gene 8034 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 108 total — 1 likely-pathogenic
  • MANE Select transcript: NM_152707

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10986
Approved symbolSLC25A16
Namesolute carrier family 25 member 16
Location10q21.3
Locus typegene with protein product
StatusApproved
AliasesGDA, D10S105E, HGT.1, ML7
Ensembl geneENSG00000122912
Ensembl biotypeprotein_coding
OMIM139080
Entrez8034

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000265870, ENST00000439904, ENST00000474927, ENST00000491102, ENST00000493963, ENST00000608053, ENST00000609923, ENST00000873655, ENST00000873656, ENST00000873657, ENST00000966724, ENST00000966725, ENST00000966726

RefSeq mRNA: 6 — MANE Select: NM_152707 NM_001324312, NM_001324313, NM_001324314, NM_001324315, NM_001324317, NM_152707

CCDS: CCDS7280

Canonical transcript exons

ENST00000609923 — 9 exons

ExonStartEnd
ENSE000013731436852724668527523
ENSE000035055226849344968493570
ENSE000037032206850363268503695
ENSE000037067426847799868483588
ENSE000037077556848714468487212
ENSE000037080776849313268493198
ENSE000037084066851675168516843
ENSE000037098736848846768488629
ENSE000037105356850658568506718

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 89.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.2197 / max 203.0742, expressed in 1810 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1097649.13941786
1097634.90291713
1097620.6479375
1097610.5104255
1097600.01916

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
jejunal mucosaUBERON:000039989.33gold quality
right lobe of liverUBERON:000111488.06gold quality
metanephros cortexUBERON:001053387.36gold quality
liverUBERON:000210786.83gold quality
adipose tissueUBERON:000101386.59gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.45gold quality
mammary glandUBERON:000191186.32gold quality
thoracic mammary glandUBERON:000520086.31gold quality
colonic epitheliumUBERON:000039786.20gold quality
mammary ductUBERON:000176586.20gold quality
connective tissueUBERON:000238485.95gold quality
corpus epididymisUBERON:000435985.94gold quality
duodenumUBERON:000211485.86gold quality
pigmented layer of retinaUBERON:000178285.77gold quality
tibiaUBERON:000097985.74gold quality
cauda epididymisUBERON:000436085.47gold quality
caput epididymisUBERON:000435885.11gold quality
body of pancreasUBERON:000115084.91gold quality
postcentral gyrusUBERON:000258184.83gold quality
apex of heartUBERON:000209884.55gold quality
upper lobe of left lungUBERON:000895284.34gold quality
epithelium of mammary glandUBERON:000324484.24gold quality
upper lobe of lungUBERON:000894884.06gold quality
hindlimb stylopod muscleUBERON:000425283.99gold quality
endothelial cellCL:000011583.97silver quality
subcutaneous adipose tissueUBERON:000219083.93gold quality
parietal lobeUBERON:000187283.82gold quality
mucosa of sigmoid colonUBERON:000499383.81gold quality
prostate glandUBERON:000236783.75gold quality
substantia nigra pars compactaUBERON:000196583.73gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting SLC25A16, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-607799.9968.042299
HSA-MIR-366299.9973.825684
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-1213699.9872.815713
HSA-MIR-433-3P99.9869.371203
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-365899.9673.874379
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-9-3P99.9670.882068
HSA-MIR-96-5P99.9572.802140

Literature-anchored findings (GeneRIF, showing 2)

  • Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)
  • The authors findings report an extreme rare missense mutation in SLC25A1 which supports the causality of this variant for autosomal recessive form of isolated fingernail dysplasia. (PMID:28504827)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioslc25a16ENSDARG00000057287
mus_musculusSlc25a16ENSMUSG00000071253
rattus_norvegicusSlc25a16ENSRNOG00000000387

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), 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

Mitochondrial coenzyme A transporter SLC25A16P16260 (reviewed: P16260)

Alternative names: Graves disease autoantigen, Graves disease carrier protein, Graves’ didease protein, Mitochondrial solute carrier protein homolog, Solute carrier family 25 member 16

All UniProt accessions (5): P16260, V9GY06, V9GYA5, V9GYB8, V9GZ24

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial inner membrane transporter that regulates coenzyme A homeostasis between cytosol and mitochondria. Could mediate the import of coenzyme A from the cytosol into the mitochondrial matrix. Alternatively, it could function in the export of 3’-dephospho-CoA from the mitochondrial matrix to the cytosol.

Subcellular location. Mitochondrion inner membrane.

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

RefSeq proteins (6): NP_001311241, NP_001311242, NP_001311243, NP_001311244, NP_001311246, NP_689920* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002067MCPFamily
IPR002167GDC-likeFamily
IPR018108MCP_transmembraneRepeat
IPR023395MCP_dom_sfHomologous_superfamily

Pfam: PF00153

Catalyzed reactions (Rhea), 2 shown:

  • ADP(out) + CoA(in) = ADP(in) + CoA(out) (RHEA:72839)
  • 3’-dephospho-CoA(in) + ADP(out) = 3’-dephospho-CoA(out) + ADP(in) (RHEA:72843)

UniProt features (17 total): sequence conflict 7, transmembrane region 6, repeat 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P16260-F185.090.53

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-199220Vitamin B5 (pantothenate) metabolism

MSigDB gene sets: 335 (showing top): GAANYNYGACNY_UNKNOWN, TGCACTT_MIR519C_MIR519B_MIR519A, MODULE_418, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, chr10q21, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, MODULE_503, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, RODRIGUES_NTN1_TARGETS_DN, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, MODULE_195

GO Biological Process (4): mitochondrial transport (GO:0006839), pantothenate metabolic process (GO:0015939), mitochondrial coenzyme A transmembrane transport (GO:1990559), transmembrane transport (GO:0055085)

GO Molecular Function (2): coenzyme A transmembrane transporter activity (GO:0015228), antiporter activity (GO:0015297)

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

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of water-soluble vitamins and cofactors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
coenzyme A transmembrane transport2
intracellular transport1
modified amino acid metabolic process1
monocarboxylic acid metabolic process1
transport1
cellular process1
organophosphate ester transmembrane transporter activity1
nucleobase-containing compound transmembrane transporter activity1
sulfur compound transmembrane transporter activity1
secondary active transmembrane transporter activity1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
cellular anatomical structure1

Protein interactions and networks

STRING

1718 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC25A16CSO75390819
SLC25A16TRIM13O60858790
SLC25A16MTCH2Q9Y6C9782
SLC25A16MTCH1Q9NZJ7781
SLC25A16CD274Q9NZQ7576
SLC25A16PAEPP09466576
SLC25A16TP53P04637541
SLC25A16CD8AP01732528
SLC25A16CTLA4P16410507
SLC25A16GAPDHP00354500
SLC25A16CD4P01730477
SLC25A16MTUS1Q9ULD2473
SLC25A16MTUS2Q5JR59473
SLC25A16PDCD1Q15116472
SLC25A16TBL1XO60907468

IntAct

56 interactions, top by confidence:

ABTypeScore
TOR1AIP2TMEM223psi-mi:“MI:0914”(association)0.530
CNDP1POTEFpsi-mi:“MI:0914”(association)0.530
DKK3NME4psi-mi:“MI:0914”(association)0.530
FAM131BAURKApsi-mi:“MI:0914”(association)0.530
HLA-DPA1TYW5psi-mi:“MI:0914”(association)0.530
PDCD1RTL8Cpsi-mi:“MI:0914”(association)0.530
SYPAPBB1psi-mi:“MI:0914”(association)0.530
GALNSCLGNpsi-mi:“MI:0914”(association)0.530
PDCD1TMEM223psi-mi:“MI:0914”(association)0.350
HLA-DPA1GXYLT2psi-mi:“MI:0914”(association)0.350
NRG1HS6ST1psi-mi:“MI:0914”(association)0.350
EDEM2HACD1psi-mi:“MI:0914”(association)0.350
SYPAPBB1psi-mi:“MI:0914”(association)0.350
PPP6R2POLRMTpsi-mi:“MI:0914”(association)0.350
CD79BGOLIM4psi-mi:“MI:0914”(association)0.350
TPP1NME4psi-mi:“MI:0914”(association)0.350
RNF126CAPN15psi-mi:“MI:0914”(association)0.350
MGARPBTAF1psi-mi:“MI:0914”(association)0.350
HLA-DRATMEM223psi-mi:“MI:0914”(association)0.350
LRRC55TMEM120Bpsi-mi:“MI:0914”(association)0.350
DNAJA2DENND11psi-mi:“MI:0914”(association)0.350
GPR182METTL15psi-mi:“MI:0914”(association)0.350
DGCR2CCDC85Cpsi-mi:“MI:0914”(association)0.350
DKK3MYO9Apsi-mi:“MI:0914”(association)0.350
RAMP3GOLIM4psi-mi:“MI:0914”(association)0.350
GPR12TLCD2psi-mi:“MI:0914”(association)0.350

BioGRID (82): SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS), SLC25A16 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D6N272, A1DI57, A2R5A0, A4RF23, A6RF73, A6SL61, A7ER02, B4FIJ0, G3XP90, G3YAF3, G3YD89, O04619, O13844, O65023, P0C546, P16260, Q01888, Q05AQ3, Q0CEN9, Q0P483, Q0UUH1, Q1E7P0, Q1LZB3, Q29RM1, Q2UCW8, Q3TZX3, Q4X022, Q5AVW1, Q5IS35, Q5NVC1, Q5PQ27, Q6AYL0, Q6P036, Q7K566, Q7S2H8, Q86VD7, Q8BZ09, Q8C0K5, Q8R0Y8, Q8RWA5

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance81
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
224813NM_152707.4(SLC25A16):c.793C>T (p.Arg265Cys)Likely pathogenic

SpliceAI

4728 predictions. Top by Δscore:

VariantEffectΔscore
10:68487138:ACTT:Adonor_loss1.0000
10:68487139:CTTA:Cdonor_loss1.0000
10:68487140:TTA:Tdonor_loss1.0000
10:68487141:TA:Tdonor_loss1.0000
10:68487142:A:ACdonor_gain1.0000
10:68487142:A:Cdonor_loss1.0000
10:68487142:ACAGG:Adonor_gain1.0000
10:68487143:C:CAdonor_gain1.0000
10:68487143:CA:Cdonor_gain1.0000
10:68487143:CAGG:Cdonor_gain1.0000
10:68487143:CAGGC:Cdonor_gain1.0000
10:68487208:GGTAG:Gacceptor_gain1.0000
10:68487209:GTAG:Gacceptor_gain1.0000
10:68487210:TAG:Tacceptor_gain1.0000
10:68487210:TAGC:Tacceptor_loss1.0000
10:68487211:AG:Aacceptor_gain1.0000
10:68487211:AGCT:Aacceptor_loss1.0000
10:68487212:GCTA:Gacceptor_loss1.0000
10:68487213:C:CCacceptor_gain1.0000
10:68487213:CT:Cacceptor_loss1.0000
10:68488465:A:ACdonor_gain1.0000
10:68488466:C:CCdonor_gain1.0000
10:68488627:CAC:Cacceptor_gain1.0000
10:68493482:T:TAdonor_gain1.0000
10:68503620:AACT:Adonor_gain1.0000
10:68503621:A:Cdonor_gain1.0000
10:68503691:ATTAA:Aacceptor_gain1.0000
10:68503692:TTAA:Tacceptor_gain1.0000
10:68503693:TAA:Tacceptor_gain1.0000
10:68503694:AA:Aacceptor_gain1.0000

AlphaMissense

2132 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:68483474:A:CF319L0.999
10:68483474:A:TF319L0.999
10:68483476:A:GF319L0.999
10:68483485:C:GA316P0.999
10:68483524:C:GG303R0.999
10:68487207:G:TP260Q0.999
10:68488497:C:TG248D0.999
10:68488500:C:TG247D0.999
10:68488610:A:CF210L0.999
10:68488610:A:TF210L0.999
10:68488612:A:GF210L0.999
10:68488629:C:TG204D0.999
10:68493171:C:GG191R0.999
10:68493538:C:GD152H0.999
10:68493540:A:TL151H0.999
10:68493561:G:TA144E0.999
10:68503643:C:TG137E0.999
10:68506619:G:TA108E0.999
10:68506658:C:TG95E0.999
10:68506659:C:GG95R0.999
10:68506659:C:TG95R0.999
10:68516791:C:AK61N0.999
10:68516791:C:GK61N0.999
10:68516798:C:GR59P0.999
10:68516843:C:TG44D0.999
10:68527246:C:GG44R0.999
10:68527248:C:TG43E0.999
10:68483475:A:GF319S0.998
10:68483484:G:TA316E0.998
10:68483510:A:CN307K0.998

dbSNP variants (sampled 300 via entrez): RS1000052110 (10:68498416 G>A), RS1000100847 (10:68522862 C>G), RS1000114981 (10:68483909 C>A), RS1000223135 (10:68517694 C>T), RS1000239573 (10:68517448 T>C), RS1000285636 (10:68495955 G>A,C), RS1000306760 (10:68478472 T>C), RS1000396662 (10:68505732 C>T), RS1000437303 (10:68490140 C>A), RS1000468110 (10:68478209 T>C), RS1000536418 (10:68522614 G>A,T), RS1000627814 (10:68511222 C>T), RS1000760165 (10:68493455 A>G), RS1000775572 (10:68491486 A>T), RS1000802498 (10:68525480 GTCTC>G,GTC)

Disease associations

OMIM: gene MIM:139080 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST000816_1Suicidal ideation7.000000e-06
GCST000816_2Suicidal ideation8.000000e-07
GCST90020028_78Hip circumference adjusted for BMI9.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004320suicidal ideation
EFO:0008039BMI-adjusted hip circumference

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

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression7
Acetaminophenincreases expression, decreases expression3
Panobinostataffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
urushioldecreases expression1
testosterone enanthateaffects expression1
bisphenol Adecreases expression1
O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphateaffects expression, affects response to substance1
arseniteaffects binding, decreases reaction1
sodium arseniteincreases expression1
di-n-butylphosphoric acidaffects expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sdecreases methylation1
Sunitinibincreases expression1
Vorinostataffects cotreatment, increases expression1
Benzo(a)pyrenedecreases expression1
Formaldehydeincreases expression1
Hydrogen Peroxideincreases expression1
Methyl Methanesulfonateincreases expression1
Progesteroneincreases expression1
Quercetindecreases expression1
Seleniumaffects cotreatment, decreases expression1
Testosteronedecreases expression1
Vitamin Edecreases expression, affects cotreatment1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideaffects expression1
Zidovudineincreases expression1
Isotretinoindecreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4CQHCT116-SLC25A16-KO-c4Cancer cell lineMale
CVCL_D4CRHCT116-SLC25A16-KO-c7Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.