SCLY

gene
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Also known as SCL

Summary

SCLY (selenocysteine lyase, HGNC:18161) is a protein-coding gene on chromosome 2q37.3, encoding Selenocysteine lyase (Q96I15). Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium.

Selenocysteine lyase (SCLY; EC 4.4.1.16) catalyzes the pyridoxal 5-prime phosphate-dependent conversion of L-selenocysteine to L-alanine and elemental selenium (Mihara et al., 2000 [PubMed 10692412]).

Source: NCBI Gene 51540 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 90 total
  • Druggable target: yes
  • MANE Select transcript: NM_016510

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18161
Approved symbolSCLY
Nameselenocysteine lyase
Location2q37.3
Locus typegene with protein product
StatusApproved
AliasesSCL
Ensembl geneENSG00000132330
Ensembl biotypeprotein_coding
OMIM611056
Entrez51540

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 15 protein_coding, 6 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000254663, ENST00000409736, ENST00000412508, ENST00000413463, ENST00000416757, ENST00000423324, ENST00000431487, ENST00000433750, ENST00000437134, ENST00000440143, ENST00000443532, ENST00000446202, ENST00000450965, ENST00000463433, ENST00000480357, ENST00000480859, ENST00000482031, ENST00000487197, ENST00000497256, ENST00000497951, ENST00000651534, ENST00000904188, ENST00000904189, ENST00000904190, ENST00000904191, ENST00000940678

RefSeq mRNA: 1 — MANE Select: NM_016510 NM_016510

CCDS: CCDS2524

Canonical transcript exons

ENST00000254663 — 12 exons

ExonStartEnd
ENSE00001623065238061001238061143
ENSE00001914431238098202238099413
ENSE00003493278238083248238083354
ENSE00003520822238082045238082209
ENSE00003521332238093861238093944
ENSE00003551615238096801238096876
ENSE00003580996238064357238064469
ENSE00003592015238069297238069477
ENSE00003625048238091218238091254
ENSE00003627610238081709238081836
ENSE00003628860238068065238068165
ENSE00003635770238094420238094522

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 92.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6852 / max 54.6202, expressed in 1718 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
263198.13201705
263200.5531315

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111492.25gold quality
body of pancreasUBERON:000115088.82gold quality
granulocyteCL:000009485.99gold quality
right hemisphere of cerebellumUBERON:001489085.59gold quality
cerebellar hemisphereUBERON:000224585.20gold quality
cerebellar cortexUBERON:000212984.98gold quality
left testisUBERON:000453384.73gold quality
right testisUBERON:000453484.62gold quality
pancreasUBERON:000126484.10gold quality
mucosa of transverse colonUBERON:000499183.43gold quality
C1 segment of cervical spinal cordUBERON:000646982.04gold quality
testisUBERON:000047381.83gold quality
monocyteCL:000057681.78gold quality
cerebellumUBERON:000203781.69gold quality
ganglionic eminenceUBERON:000402381.38gold quality
leukocyteCL:000073881.27gold quality
stromal cell of endometriumCL:000225581.15gold quality
islet of LangerhansUBERON:000000681.11gold quality
right lobe of thyroid glandUBERON:000111981.11gold quality
body of uterusUBERON:000985381.11gold quality
small intestine Peyer’s patchUBERON:000345481.06gold quality
mononuclear cellCL:000084281.02gold quality
apex of heartUBERON:000209880.89gold quality
metanephros cortexUBERON:001053380.69gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.39gold quality
ventricular zoneUBERON:000305380.36gold quality
left uterine tubeUBERON:000130380.02gold quality
lower esophagusUBERON:001347380.02gold quality
lower esophagus muscularis layerUBERON:003583380.02gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.87gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-MTAB-7606no361.93
E-ANND-3no3.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting SCLY, 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-6825-5P99.9669.813431
HSA-MIR-9-3P99.9670.882068
HSA-MIR-806399.9169.763146
HSA-MIR-7845-5P99.8864.88771
HSA-MIR-202-5P99.7867.65991
HSA-MIR-431999.7669.832586
HSA-MIR-432099.7565.80793
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-368599.6268.831621
HSA-MIR-497-3P99.6169.711990
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-141-5P99.5767.86897
HSA-MIR-312899.5067.851258
HSA-MIR-569799.3967.741249
HSA-MIR-125A-5P99.3670.591640
HSA-MIR-125B-5P99.3670.361662
HSA-MIR-488-5P99.2868.12821
HSA-MIR-397899.2468.392201
HSA-MIR-670-3P99.0368.882404
HSA-MIR-181A-2-3P98.9167.601168
HSA-MIR-442498.9170.331145
HSA-MIR-38498.7167.341229
HSA-MIR-518C-5P98.5369.201640
HSA-MIR-6509-3P98.3267.331343
HSA-MIR-6732-3P98.1767.52802
HSA-MIR-299-3P97.7366.67773
HSA-MIR-89097.4768.67982
HSA-MIR-447597.3666.95761

Literature-anchored findings (GeneRIF, showing 4)

  • PMID:10692412 concerns mostly mouse selenocysteine lyase, however, refers to the sequence of the N-terminal region of putative human protein. (PMID:10692412)
  • Results confirm that HCV core protein is associated with specific changes in mRNA expression, including the gene for selenocysteine lyase, which may be involved in the pathophysiology of hepatocellular carcinoma. (PMID:16925092)
  • A reaction mechanism whereby the Selenocysteine over Cysteine specificity is achieved using a combination of chemical and physico-mechanical control mechanisms. (PMID:22291978)
  • the X-ray crystal structure of human selenocysteine lyase and the key residue that provides the selenocysteine specificity (PMID:22295093)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosclyENSDARG00000073813
mus_musculusSclyENSMUSG00000026307
rattus_norvegicusSclyENSRNOG00000020083
caenorhabditis_elegansWBGENE00017442

Paralogs (1): NFS1 (ENSG00000244005)

Protein

Protein identifiers

Selenocysteine lyaseQ96I15 (reviewed: Q96I15)

All UniProt accessions (12): Q96I15, A0A0A0MQU4, C9JNL5, F8WBU3, F8WCL3, H7C1N7, H7C277, H7C280, H7C2H3, H7C2M1, H7C3V9, H7C4A1

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm. Cytosol.

Induction. Up-regulated in acute glomerulonephritis. Regulated by JUN/AP-1.

Similarity. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96I15-11yes
Q96I15-22

RefSeq proteins (1): NP_057594* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000192Aminotrans_V_domDomain
IPR015421PyrdxlP-dep_Trfase_majorHomologous_superfamily
IPR015422PyrdxlP-dep_Trfase_smallHomologous_superfamily
IPR015424PyrdxlP-dep_TrfaseHomologous_superfamily
IPR016454Cysteine_dSaseFamily

Pfam: PF00266

Enzyme classification (BRENDA):

  • EC 4.4.1.16 — selenocysteine lyase (BRENDA: 19 organisms, 40 substrates, 34 inhibitors, 18 Km, 8 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
L-SELENOCYSTEINE0.2–9.915
L-CYSTEINE SULFINATE8.6–302
BETA-CHLORO-L-ALANINE3.11

Catalyzed reactions (Rhea), 1 shown:

  • L-selenocysteine + AH2 = hydrogenselenide + L-alanine + A + H(+) (RHEA:11632)

UniProt features (46 total): helix 16, strand 12, turn 6, modified residue 3, sequence variant 3, sequence conflict 2, chain 1, region of interest 1, active site 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
3GZDX-RAY DIFFRACTION1.8
3GZCX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96I15-F191.140.85

Functional residue map

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

Catalytic / active sites (1): 388 (s-selanylcysteine intermediate)

Post-translational modifications (3): 1, 129, 259

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-2408508Metabolism of ingested SeMet, Sec, MeSec into H2Se
R-HSA-1430728Metabolism
R-HSA-2408522Selenoamino acid metabolism
R-HSA-71291Metabolism of amino acids and derivatives

MSigDB gene sets: 130 (showing top): GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, GOBP_AMINO_ACID_CATABOLIC_PROCESS, DANG_BOUND_BY_MYC, HAMAI_APOPTOSIS_VIA_TRAIL_DN, SENESE_HDAC3_TARGETS_DN, NUYTTEN_EZH2_TARGETS_DN, BENPORATH_MYC_MAX_TARGETS, GOMF_AMINO_ACID_BINDING, GOMF_PROTEIN_DIMERIZATION_ACTIVITY

GO Biological Process (2): amino acid metabolic process (GO:0006520), L-selenocysteine catabolic process (GO:0016261)

GO Molecular Function (7): selenocysteine lyase activity (GO:0009000), amino acid binding (GO:0016597), transferase activity (GO:0016740), protein homodimerization activity (GO:0042803), vitamin B6 binding (GO:0070279), protein binding (GO:0005515), lyase activity (GO:0016829)

GO Cellular Component (4): Golgi apparatus (GO:0005794), cytosol (GO:0005829), catalytic complex (GO:1902494), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Selenoamino acid metabolism1
Metabolism of amino acids and derivatives1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
catalytic activity2
cytoplasm2
cellular anatomical structure2
primary metabolic process1
modified amino acid catabolic process1
L-amino acid catabolic process1
proteinogenic amino acid catabolic process1
carbon-sulfur lyase activity1
identical protein binding1
protein dimerization activity1
vitamin binding1
heterocyclic compound binding1
endomembrane system1
intracellular membrane-bounded organelle1
protein-containing complex1
intracellular anatomical structure1

Protein interactions and networks

STRING

1633 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCLYSEPHS2Q99611752
SCLYSEPSECSQ9HD40716
SCLYPSTKQ8IV42711
SCLYSELENOKQ9Y6D0658
SCLYSELENOMQ8WWX9645
SCLYEEFSECP57772644
SCLYSECISBP2Q96T21643
SCLYSELENOSQ9BQE4643
SCLYSEPHS1P49903634
SCLYSELENOFO60613633
SCLYSELENOPP49908626
SCLYCTHP32929589
SCLYSELENONQ9NZV5560
SCLYSELENOTP62341519
SCLYSELENOVP59797506
SCLYTRNAU1APQ9NX07506

IntAct

20 interactions, top by confidence:

ABTypeScore
CDK2CCNE2psi-mi:“MI:0914”(association)0.940
SCLYLNX2psi-mi:“MI:0915”(physical association)0.670
LNX2SCLYpsi-mi:“MI:0915”(physical association)0.670
EIF1ADNAXDpsi-mi:“MI:0914”(association)0.620
APBA3CLSTN1psi-mi:“MI:0914”(association)0.530
TERF2IPSCLYpsi-mi:“MI:0915”(physical association)0.510
CREB3SCLYpsi-mi:“MI:0915”(physical association)0.370
NcaphATP5MF-PTCD1psi-mi:“MI:0914”(association)0.350
TFGNCOA4psi-mi:“MI:0914”(association)0.350
Atp7aRTL8Cpsi-mi:“MI:0914”(association)0.350
VPS18DNAJB5psi-mi:“MI:0914”(association)0.350
Mcm3ELL2psi-mi:“MI:0914”(association)0.350
EXOSC5PAPD5psi-mi:“MI:0914”(association)0.350
RANBP1RGPD3psi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
MTPNPLCG1psi-mi:“MI:0914”(association)0.350
SCLYTERF2IPpsi-mi:“MI:0915”(physical association)0.000
SCLYpsi-mi:“MI:0915”(physical association)0.000

BioGRID (48): CCBL1 (Co-fractionation), HYI (Co-fractionation), IDE (Co-fractionation), NUTF2 (Co-fractionation), SCLY (Co-fractionation), SCLY (Co-fractionation), SCLY (Co-fractionation), SCLY (Co-fractionation), SCLY (Co-fractionation), SCLY (Co-fractionation), SCLY (Co-fractionation), WDR1 (Co-fractionation), SCLY (Two-hybrid), SCLY (Two-hybrid), SCLY (Affinity Capture-MS)

ESM2 similar proteins: A2VDS1, A4SP14, A4VNY2, A4XY43, A5GFY8, A6V0U8, A7H804, A7MBC0, A8GHY3, B0VD51, B0VNW2, B0YLW6, B2HZI5, B4UCP2, B7H3H0, B7I5Q3, B7UWH7, B8JC53, C1DE68, O31269, O43175, O49543, O60028, O74351, O75600, O88986, P0DN31, P25374, Q02RW8, Q0P5L8, Q10G56, Q1H361, Q2INI7, Q5BJY6, Q5R7M2, Q5U4Q9, Q60HD7, Q61753, Q66IQ6, Q68FT9

Diamond homologs: A1KUK1, A2VDS1, A4WDB1, A5I4Z9, A6TCF1, A7FWJ9, A7H804, A7MU48, A7ZPX4, A8A336, A8EYH9, A8F204, A8GHY3, A8GNU0, A8GSG4, A8GWB2, A9M029, A9MHJ4, A9N1X5, B0BXX6, B0YLW6, B1IWD1, B1LNI6, B1XB05, B2US50, B4T0S2, B4TDB6, B4TRX5, B4UCP2, B5BAW6, B5F1C0, B5FR85, B5R5A2, B5RD12, B5XNJ7, B5Z104, B6I5A2, B6JKF2, B7LDC2, B7M7N3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance78
Likely benign6
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2724 predictions. Top by Δscore:

VariantEffectΔscore
2:238064352:TTCA:Tacceptor_loss1.0000
2:238064353:TCA:Tacceptor_loss1.0000
2:238064355:A:AGacceptor_gain1.0000
2:238064355:A:Tacceptor_loss1.0000
2:238064355:AG:Aacceptor_gain1.0000
2:238064356:G:GTacceptor_gain1.0000
2:238064356:GG:Gacceptor_gain1.0000
2:238064356:GGA:Gacceptor_gain1.0000
2:238064356:GGAA:Gacceptor_gain1.0000
2:238064356:GGAAA:Gacceptor_gain1.0000
2:238064465:AGCAG:Adonor_loss1.0000
2:238064466:GCAG:Gdonor_gain1.0000
2:238064468:AGG:Adonor_loss1.0000
2:238064468:AGGT:Adonor_loss1.0000
2:238064469:GGTA:Gdonor_loss1.0000
2:238064471:T:Adonor_loss1.0000
2:238068053:T:TAacceptor_gain1.0000
2:238073848:G:GGdonor_gain1.0000
2:238081707:A:AGacceptor_gain1.0000
2:238081707:AGC:Aacceptor_gain1.0000
2:238081708:G:GCacceptor_gain1.0000
2:238081708:GCG:Gacceptor_gain1.0000
2:238082041:TCAGC:Tacceptor_loss1.0000
2:238082042:CAGCC:Cacceptor_loss1.0000
2:238082043:A:AGacceptor_gain1.0000
2:238082043:A:Cacceptor_loss1.0000
2:238082044:G:Aacceptor_loss1.0000
2:238082044:G:GAacceptor_gain1.0000
2:238082044:GC:Gacceptor_gain1.0000
2:238082044:GCC:Gacceptor_gain1.0000

AlphaMissense

2909 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:238098266:A:CS417R0.996
2:238098268:C:AS417R0.996
2:238098268:C:GS417R0.996
2:238064370:G:CD35H0.995
2:238064372:C:AD35E0.994
2:238064372:C:GD35E0.994
2:238069428:C:AH145Q0.993
2:238069428:C:GH145Q0.993
2:238082208:A:TK259M0.993
2:238083348:G:CR293T0.993
2:238091227:C:AN298K0.992
2:238091227:C:GN298K0.992
2:238098318:T:CL434P0.992
2:238064371:A:TD35V0.991
2:238064447:T:AN60K0.991
2:238064447:T:GN60K0.991
2:238083348:G:TR293M0.991
2:238083349:G:CR293S0.991
2:238083349:G:TR293S0.991
2:238094494:C:AN360K0.991
2:238094494:C:GN360K0.991
2:238082129:G:CD233H0.990
2:238082130:A:TD233V0.990
2:238082209:G:CK259N0.990
2:238082209:G:TK259N0.990
2:238069433:C:TS147F0.989
2:238093919:G:CR327P0.989
2:238064371:A:CD35A0.988
2:238069426:C:GH145D0.988
2:238081826:G:TG201V0.988

dbSNP variants (sampled 300 via entrez): RS1000009707 (2:238087096 A>G), RS1000142871 (2:238064269 C>T), RS1000267118 (2:238085737 A>G), RS1000296805 (2:238085534 C>T), RS1000297315 (2:238066479 G>A,T), RS1000371579 (2:238085444 T>G), RS1000405249 (2:238084125 G>C), RS1000485341 (2:238091716 A>G), RS1000550200 (2:238066231 C>A), RS1000598253 (2:238084080 C>T), RS1000616715 (2:238077891 G>C), RS1000650988 (2:238083739 G>A), RS1000688461 (2:238079601 T>G), RS1000796617 (2:238096757 C>G,T), RS1000859908 (2:238079931 A>G)

Disease associations

OMIM: gene MIM:611056 | 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: yes

ChEMBL targets (1): CHEMBL6066434 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.05Kd890.7nMCHEMBL5653589
6.05ED50890.7nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149352: Binding affinity to human SCLY incubated for 45 mins by Kinobead based pull down assaykd0.8907uM

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression, increases methylation3
sodium arsenitedecreases expression2
Smokedecreases expression, decreases reaction2
Tetrachlorodibenzodioxindecreases expression2
Tretinoindecreases expression2
Cyclosporinedecreases expression, increases expression2
afuresertibdecreases expression1
sodium arsenatedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chloridedecreases expression1
potassium chromate(VI)decreases expression, affects cotreatment1
4-aminophenylarsenoxideaffects binding, decreases reaction1
epigallocatechin gallateaffects cotreatment, decreases expression1
K 7174decreases expression1
Decitabinedecreases expression, decreases reaction1
Arsenic Trioxideaffects binding, decreases reaction1
Acetaminophendecreases expression1
Cisplatindecreases expression1
Demecolcinedecreases expression1
Dibutyl Phthalateaffects cotreatment, increases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Hydrogen Peroxideaffects expression1
Tetradecanoylphorbol Acetateaffects cotreatment, increases expression1
Vincristinedecreases expression1
Antirheumatic Agentsdecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652394BindingBinding affinity to human SCLY incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.