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Atlas / Gene / SLC66A2

SLC66A2

gene
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Also known as FLJ22378

Summary

SLC66A2 (solute carrier family 66 member 2, HGNC:26188) is a protein-coding gene on chromosome 18q23, encoding Solute carrier family 66 member 2 (Q8N2U9).

Predicted to be involved in phospholipid translocation and retrograde transport, endosome to Golgi. Predicted to be located in cytosol and membrane. Predicted to be active in endosome and trans-Golgi network.

Source: NCBI Gene 80148 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 72 total — 1 pathogenic
  • MANE Select transcript: NM_025078

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26188
Approved symbolSLC66A2
Namesolute carrier family 66 member 2
Location18q23
Locus typegene with protein product
StatusApproved
AliasesFLJ22378
Ensembl geneENSG00000122490
Ensembl biotypeprotein_coding
Entrez80148

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 18 protein_coding, 5 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000351365, ENST00000357575, ENST00000397778, ENST00000466449, ENST00000469369, ENST00000474967, ENST00000478144, ENST00000494607, ENST00000589000, ENST00000589452, ENST00000590381, ENST00000590895, ENST00000591964, ENST00000593030, ENST00000905913, ENST00000905914, ENST00000905915, ENST00000905916, ENST00000905917, ENST00000905918, ENST00000905919, ENST00000905920, ENST00000922814, ENST00000954268, ENST00000954269, ENST00000954270, ENST00000954271, ENST00000954272

RefSeq mRNA: 3 — MANE Select: NM_025078 NM_001146343, NM_001146345, NM_025078

CCDS: CCDS12020, CCDS54192, CCDS54193

Canonical transcript exons

ENST00000397778 — 6 exons

ExonStartEnd
ENSE000015422017990242079904183
ENSE000022820507995158179951653
ENSE000028037857995072479951025
ENSE000035923977994332979943462
ENSE000036298707993396979934022
ENSE000036762357991918479919400

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 98.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5582 / max 222.6898, expressed in 1818 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
17266220.55821818

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111498.01gold quality
right testisUBERON:000453497.26gold quality
right lobe of thyroid glandUBERON:000111997.20gold quality
left testisUBERON:000453397.20gold quality
lower esophagus mucosaUBERON:003583496.90gold quality
left lobe of thyroid glandUBERON:000112096.78gold quality
right frontal lobeUBERON:000281096.65gold quality
anterior cingulate cortexUBERON:000983596.56gold quality
cingulate cortexUBERON:000302796.53gold quality
tibial nerveUBERON:000132396.07gold quality
thyroid glandUBERON:000204696.04gold quality
liverUBERON:000210795.50gold quality
gastrocnemiusUBERON:000138895.43gold quality
amygdalaUBERON:000187695.41gold quality
apex of heartUBERON:000209895.33gold quality
prefrontal cortexUBERON:000045195.04gold quality
right hemisphere of cerebellumUBERON:001489094.99gold quality
Brodmann (1909) area 9UBERON:001354094.98gold quality
skin of legUBERON:000151194.87gold quality
mucosa of transverse colonUBERON:000499194.74gold quality
nucleus accumbensUBERON:000188294.73gold quality
putamenUBERON:000187494.57gold quality
olfactory segment of nasal mucosaUBERON:000538694.52gold quality
testisUBERON:000047394.48gold quality
neocortexUBERON:000195094.25gold quality
cerebellar hemisphereUBERON:000224594.24gold quality
skin of abdomenUBERON:000141694.22gold quality
omental fat padUBERON:001041494.20gold quality
frontal cortexUBERON:000187094.18gold quality
peritoneumUBERON:000235894.14gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting SLC66A2, 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-4262100.0073.263931
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-118499.9968.191458
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-6871-3P99.4368.85741
HSA-MIR-431699.3765.751360
HSA-MIR-429199.2068.882969
HSA-MIR-1911-3P99.1566.17528
HSA-MIR-312599.1468.492269
HSA-MIR-485-5P99.1064.781889
HSA-MIR-6884-5P99.1064.501987
HSA-MIR-447899.0765.162320
HSA-MIR-391698.9968.042155
HSA-MIR-6859-5P98.9968.072049
HSA-MIR-392998.3265.581026
HSA-MIR-397798.0068.171500
HSA-MIR-197297.6767.381172
HSA-MIR-10400-3P97.2964.66597
HSA-MIR-467497.2964.62597
HSA-MIR-428697.2064.371587
HSA-MIR-4632-3P96.2658.52123
HSA-MIR-6788-3P94.5066.1768

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioSLC66A2ENSDARG00000112922
mus_musculusSlc66a2ENSMUSG00000034006
rattus_norvegicusSlc66a2ENSRNOG00000059215
drosophila_melanogasterCG13784FBGN0031897
caenorhabditis_elegansT19A6.1WBGENE00011827

Protein

Protein identifiers

Solute carrier family 66 member 2 — Q8N2U9 (reviewed: Q8N2U9)

Alternative names: PQ-loop repeat-containing protein 1

All UniProt accessions (6): Q8N2U9, K7EMG2, K7EQ76, K7ERD3, K7ERV4, X6R488

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (3)

UniProt IDNamesCanonical?
Q8N2U9-11yes
Q8N2U9-22
Q8N2U9-33

RefSeq proteins (3): NP_001139815, NP_001139817, NP_079354* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006603PQ-loop_rptRepeat
IPR052241SLC66/Scramblase_ANY1Family

Pfam: PF04193

UniProt features (14 total): transmembrane region 6, splice variant 3, domain 2, chain 1, sequence variant 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N2U9-F185.670.56

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 110

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 149 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, CREB_Q4, GOCC_TRANS_GOLGI_NETWORK, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_LIPID_LOCALIZATION

GO Biological Process (2): retrograde transport, endosome to Golgi (GO:0042147), phospholipid translocation (GO:0045332)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): endosome (GO:0005768), trans-Golgi network (GO:0005802), cytosol (GO:0005829), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
intercellular transport1
endosomal transport1
cytosolic transport1
phospholipid transport1
lipid translocation1
binding1
endomembrane system1
cytoplasmic vesicle1
Golgi apparatus subcompartment1
cytoplasm1

Protein interactions and networks

STRING

430 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC66A2RBFAQ8N0V3594
SLC66A2FAM89BQ8N5H3576
SLC66A2TXNL4AP83876566
SLC66A2ATP9BO43861524
SLC66A2PRPF38BQ5VTL8506
SLC66A2ZNF407Q9C0G0505
SLC66A2SCOCQ9UIL1497
SLC66A2HSBP1L1C9JCN9490
SLC66A2ZNF516Q92618488
SLC66A2ADNP2Q6IQ32487
SLC66A2RIIAD1A6NNX1466
SLC66A2DLGAP3O95886465
SLC66A2KCNG2Q9UJ96452
SLC66A2ATP6V1DQ9Y5K8451
SLC66A2CTDP1Q9Y5B0441

IntAct

72 interactions, top by confidence:

ABTypeScore
SLC66A2AQP6psi-mi:“MI:0915”(physical association)0.560
SLC66A2GJA8psi-mi:“MI:0915”(physical association)0.560
FBLN1SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2psi-mi:“MI:0915”(physical association)0.560
IL10RASLC66A2psi-mi:“MI:0915”(physical association)0.560
ZFYVE27SLC66A2psi-mi:“MI:0915”(physical association)0.560
TMEM44SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2SLC25A46psi-mi:“MI:0915”(physical association)0.560
STX12SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC10A6SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2DIABLOpsi-mi:“MI:0915”(physical association)0.560
AQP6SLC66A2psi-mi:“MI:0915”(physical association)0.560
CLCN7SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2GPR152psi-mi:“MI:0915”(physical association)0.560
GJA8SLC66A2psi-mi:“MI:0915”(physical association)0.560
MFSD14BSLC66A2psi-mi:“MI:0915”(physical association)0.560
CD79ASLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2FUNDC2psi-mi:“MI:0915”(physical association)0.560
KCNK5SLC66A2psi-mi:“MI:0915”(physical association)0.560
MGLLSLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2TMEM80psi-mi:“MI:0915”(physical association)0.560
SLC35E3SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC10A1SLC66A2psi-mi:“MI:0915”(physical association)0.560
SLC66A2RHBDD1psi-mi:“MI:0915”(physical association)0.560
SLC66A2BEST2psi-mi:“MI:0915”(physical association)0.560
ADH5SLC66A2psi-mi:“MI:0915”(physical association)0.370
PACSIN1SLC66A2psi-mi:“MI:0915”(physical association)0.000
FBLN1SLC66A2psi-mi:“MI:0915”(physical association)0.000

BioGRID (32): PQLC1 (Affinity Capture-RNA), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), PQLC1 (Two-hybrid), RHBDD1 (Two-hybrid), TMEM44 (Two-hybrid), SLC10A6 (Two-hybrid), HIATL1 (Two-hybrid)

ESM2 similar proteins: A0A097ZPD8, A0A0E3D8M2, A0A0E3D8Q2, A0A0F7TZE0, A0A0U5GIU9, A0A140JWT2, A0A1B7YCX1, A0A1E1FFM9, A0A1Y0BRF5, A0A2I1BT01, A0A2I6PJ07, A0A2P1DP74, A0A3G9H8P0, A0A3T0ZHJ5, A0A455RAK9, A0A8D5M7T9, A9JPE3, B6HV37, E3UBL6, E9F5E8, J7FIJ6, K2RU64, M1VJS5, P0DY23, P24390, P33946, P35402, P48583, P9WEQ3, P9WEX1, P9WEX7, P9WEY0, Q0VCC1, Q15FB1, Q4WBI3, Q4WLD2, Q569A6, Q5M880, Q5U305, Q5XHA2

Diamond homologs: Q0VCC1, Q5M880, Q6NRS2, Q80XM9, Q8N2U9, Q03687

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance49
Likely benign7
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
202227GRCh37/hg19 18q23(chr18:74241380-78013620)x1Pathogenic

SpliceAI

2209 predictions. Top by Δscore:

VariantEffectΔscore
18:79904181:ATGC:Aacceptor_loss1.0000
18:79904182:TG:Tacceptor_gain1.0000
18:79904183:GC:Gacceptor_loss1.0000
18:79904184:C:CAacceptor_loss1.0000
18:79904184:C:CCacceptor_gain1.0000
18:79904185:T:Cacceptor_loss1.0000
18:79930226:A:ACdonor_gain1.0000
18:79930227:C:CCdonor_gain1.0000
18:79943324:CCAA:Cdonor_loss1.0000
18:79943326:AACC:Adonor_loss1.0000
18:79943327:ACC:Adonor_loss1.0000
18:79943328:CCTGT:Cdonor_loss1.0000
18:79943458:CAAAC:Cacceptor_gain1.0000
18:79943463:C:CAacceptor_loss1.0000
18:79943463:C:CCacceptor_gain1.0000
18:79943464:T:Cacceptor_loss1.0000
18:79950719:CTTA:Cdonor_loss1.0000
18:79950720:TTACC:Tdonor_loss1.0000
18:79950721:TACCA:Tdonor_loss1.0000
18:79950722:A:ACdonor_gain1.0000
18:79950722:AC:Adonor_gain1.0000
18:79950723:C:CCdonor_gain1.0000
18:79950723:CC:Cdonor_gain1.0000
18:79950723:CCA:Cdonor_gain1.0000
18:79950723:CCAG:Cdonor_gain1.0000
18:79950723:CCAGA:Cdonor_gain1.0000
18:79904179:TGATG:Tacceptor_gain0.9900
18:79904180:GATG:Gacceptor_gain0.9900
18:79904181:ATG:Aacceptor_gain0.9900
18:79943283:ACGC:Adonor_gain0.9900

AlphaMissense

1756 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:79904141:C:AK217N0.998
18:79904141:C:GK217N0.998
18:79904164:A:GW210R0.998
18:79904164:A:TW210R0.998
18:79950780:G:CF49L0.998
18:79950780:G:TF49L0.998
18:79950782:A:GF49L0.998
18:79904102:G:CF230L0.997
18:79904102:G:TF230L0.997
18:79904104:A:GF230L0.997
18:79943423:G:CS81R0.997
18:79943423:G:TS81R0.997
18:79943425:T:GS81R0.997
18:79950781:A:GF49S0.997
18:79904162:C:AW210C0.996
18:79904162:C:GW210C0.996
18:79943447:A:CF73L0.996
18:79943447:A:TF73L0.996
18:79943449:A:GF73L0.996
18:79950726:G:CF67L0.996
18:79950726:G:TF67L0.996
18:79950728:A:GF67L0.996
18:79950744:G:CN61K0.996
18:79950744:G:TN61K0.996
18:79904103:A:GF230S0.995
18:79950781:A:CF49C0.995
18:79904156:A:CS212R0.994
18:79904156:A:TS212R0.994
18:79904158:T:GS212R0.994
18:79919374:A:GW140R0.994

dbSNP variants (sampled 300 via entrez): RS1000013244 (18:79934140 A>C), RS1000033062 (18:79940025 A>G,T), RS1000132280 (18:79947278 T>C), RS1000142429 (18:79939738 G>A), RS1000199129 (18:79919104 G>A), RS1000331093 (18:79949667 A>C,G), RS1000332531 (18:79949391 C>G,T), RS1000384184 (18:79934423 G>A,C,T), RS1000468546 (18:79949177 T>C,G), RS1000480641 (18:79938547 A>C,G), RS1000550890 (18:79902820 G>A), RS1000581201 (18:79905598 C>T), RS1000669518 (18:79948459 G>C), RS1000695954 (18:79905453 C>T), RS1000762682 (18:79948223 G>A)

Disease associations

OMIM: gene `` | 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):

StudyTraitp-value
GCST90026414_1Severe insulin-resistant type 2 diabetes4.000000e-07

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 — SLC66 Lysosomal amino acid transporters

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
Benzo(a)pyreneaffects methylation, decreases expression2
Cyclosporinedecreases expression2
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
butyraldehydeincreases expression1
Arsenicdecreases expression, increases abundance, increases expression, affects cotreatment1
Carbamazepineaffects expression1
Smokedecreases expression1
Tetrachlorodibenzodioxinaffects expression1
Tretinoindecreases expression1
Urethaneincreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1decreases expression1
Palmitic Aciddecreases expression1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_TG35HAP1 PQLC1 (-) 1Cancer cell lineMale
CVCL_XR80HAP1 PQLC1 (-) 2Cancer 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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgtopdb_interactiongwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot