HACL2

gene
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Also known as 209L8AHASILV2HMGC1269FLJ39061MGC19535HACL1L

Summary

HACL2 (2-hydroxyacyl-CoA lyase 2, HGNC:6041) is a protein-coding gene on chromosome 19p13.12, encoding 2-hydroxyacyl-CoA lyase 2 (A1L0T0). Endoplasmic reticulum 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the fatty acid alpha-oxydation in a thiamine pyrophosphate (TPP)-dependent manner.

The protein encoded by this gene shares similarity with several thiamine pyrophosphate-binding proteins identified in bacteria, yeast, and plants. The highest degree of similarity is found with bacterial acetolactate synthases (AHAS), which are enzymes that catalyze the first step in branched-chain amino acid biosynthesis.

Source: NCBI Gene 10994 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 107 total
  • Druggable target: yes
  • MANE Select transcript: NM_006844

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6041
Approved symbolHACL2
Name2-hydroxyacyl-CoA lyase 2
Location19p13.12
Locus typegene with protein product
StatusApproved
Aliases209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535, HACL1L, HACL2
Ensembl geneENSG00000105135
Ensembl biotypeprotein_coding
OMIM605770
Entrez10994

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 28 protein_coding, 6 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000263383, ENST00000524779, ENST00000525880, ENST00000527093, ENST00000531635, ENST00000533086, ENST00000533148, ENST00000533747, ENST00000534378, ENST00000534806, ENST00000596093, ENST00000598709, ENST00000599324, ENST00000600984, ENST00000862950, ENST00000862951, ENST00000862952, ENST00000862953, ENST00000862954, ENST00000862955, ENST00000862956, ENST00000862957, ENST00000862958, ENST00000862959, ENST00000862960, ENST00000862961, ENST00000862962, ENST00000862963, ENST00000924995, ENST00000924996, ENST00000953427, ENST00000953428, ENST00000953429, ENST00000953430, ENST00000953431, ENST00000953432

RefSeq mRNA: 1 — MANE Select: NM_006844 NM_006844

CCDS: CCDS12325

Canonical transcript exons

ENST00000263383 — 16 exons

ExonStartEnd
ENSE000013026631511498715115430
ENSE000013825031512492515125069
ENSE000021570831512565615125786
ENSE000034646671512337515123576
ENSE000034657261511916615119302
ENSE000034712561512269315122804
ENSE000034987521511585015115921
ENSE000035277411512311615123243
ENSE000035526951512289215123030
ENSE000035858311511640815116522
ENSE000035942861511600115116071
ENSE000036577781511556615115671
ENSE000036743351511941815119515
ENSE000036888461511788115118015
ENSE000036927531511998215120081
ENSE000036939711511615215116321

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 97.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.0367 / max 122.0122, expressed in 1792 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1796977.06381750
1796983.65471520
1796951.3155763
1796960.7304476
1796940.272399

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209897.64gold quality
right atrium auricular regionUBERON:000663195.53gold quality
mucosa of transverse colonUBERON:000499195.43gold quality
heart left ventricleUBERON:000208495.21gold quality
transverse colonUBERON:000115795.19gold quality
metanephros cortexUBERON:001053395.12gold quality
cardiac ventricleUBERON:000208294.91gold quality
right adrenal gland cortexUBERON:003582794.61gold quality
cardiac atriumUBERON:000208194.54gold quality
right lobe of thyroid glandUBERON:000111994.37gold quality
body of stomachUBERON:000116194.25gold quality
left adrenal gland cortexUBERON:003582594.25gold quality
right adrenal glandUBERON:000123394.12gold quality
muscle layer of sigmoid colonUBERON:003580594.10gold quality
pancreatic ductal cellCL:000207994.06gold quality
skin of legUBERON:000151194.05gold quality
left adrenal glandUBERON:000123493.99gold quality
left lobe of thyroid glandUBERON:000112093.91gold quality
heartUBERON:000094893.70gold quality
small intestine Peyer’s patchUBERON:000345493.65gold quality
adrenal cortexUBERON:000123593.58gold quality
right lobe of liverUBERON:000111493.57gold quality
skin of abdomenUBERON:000141693.44gold quality
thyroid glandUBERON:000204693.36gold quality
esophagus mucosaUBERON:000246993.21gold quality
nephron tubuleUBERON:000123193.12gold quality
small intestineUBERON:000210893.02gold quality
lower esophagus mucosaUBERON:003583492.87gold quality
adenohypophysisUBERON:000219692.83gold quality
adrenal glandUBERON:000236992.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting HACL2, 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-6887-3P99.6667.831778
HSA-MIR-444199.4966.563216
HSA-MIR-425199.4069.193363
HSA-MIR-6837-5P99.2565.471632
HSA-MIR-4685-5P99.2565.991563
HSA-MIR-427099.0266.261987
HSA-MIR-390898.7567.311160
HSA-MIR-6754-5P98.6065.541627
HSA-MIR-367097.8864.39763
HSA-MIR-392197.8167.451431
HSA-MIR-432997.6866.261003
HSA-MIR-4640-5P97.4266.331543
HSA-MIR-4726-5P97.2465.671299
HSA-MIR-4653-5P97.2267.721429
HSA-MIR-873-3P96.8466.09786
HSA-MIR-6508-3P96.7365.48576
HSA-MIR-286195.2465.471056

Literature-anchored findings (GeneRIF, showing 1)

  • To the best of our knowledge, this is the first report of an association between single nucleotide polymorphisms (SNPs) on ILVBL and aspirin-exacerbated respiratory disease (AERD) . SNPs on ILVBL could be promising genetic markers of this condition. (PMID:29246216)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioilvblENSDARG00000017126
mus_musculusIlvblENSMUSG00000032763
rattus_norvegicusIlvblENSRNOG00000028512
caenorhabditis_elegansWBGENE00020831

Paralogs (1): HACL1 (ENSG00000131373)

Protein

Protein identifiers

2-hydroxyacyl-CoA lyase 2A1L0T0 (reviewed: A1L0T0)

Alternative names: Acetolactate synthase-like protein, IlvB-like protein

All UniProt accessions (7): A1L0T0, E9PJS0, E9PL44, E9PNL1, M0QZX5, M0R026, M0R1B5

UniProt curated annotations — full annotation on UniProt →

Function. Endoplasmic reticulum 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the fatty acid alpha-oxydation in a thiamine pyrophosphate (TPP)-dependent manner. Involved in the phytosphingosine degradation pathway.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Expressed in all tissues tested, with highest expression in heart, pancreas and placenta.

Cofactor. Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit.

Similarity. Belongs to the TPP enzyme family.

RefSeq proteins (1): NP_006835* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000399TPP-bd_CSConserved_site
IPR011766TPP_enzyme_TPP-bdDomain
IPR012000Thiamin_PyroP_enz_cen_domDomain
IPR012001Thiamin_PyroP_enz_TPP-bd_domDomain
IPR029035DHS-like_NAD/FAD-binding_domHomologous_superfamily
IPR029061THDP-bindingHomologous_superfamily
IPR045229TPP_enzFamily

Pfam: PF00205, PF02775, PF02776

Catalyzed reactions (Rhea), 2 shown:

  • 2-hydroxyoctadecanoyl-CoA = heptadecanal + formyl-CoA (RHEA:55196)
  • (2R)-hydroxyhexadecanoyl-CoA = pentadecanal + formyl-CoA (RHEA:55212)

UniProt features (8 total): binding site 3, sequence variant 2, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A1L0T0-F194.530.89

Functional residue map

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

Ligand- & substrate-binding residues (3): 98; 521; 547

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 154 (showing top): MORF_MTA1, GOBP_LIPID_MODIFICATION, GOBP_FATTY_ACID_CATABOLIC_PROCESS, TGACCTY_ERR1_Q2, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, MORF_PPP5C, MORF_FANCG, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, CREB_Q2_01, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS, MORF_IKBKG

GO Biological Process (5): fatty acid alpha-oxidation (GO:0001561), obsolete isoleucine biosynthetic process (GO:0009097), L-valine biosynthetic process (GO:0009099), lipid metabolic process (GO:0006629), fatty acid metabolic process (GO:0006631)

GO Molecular Function (8): magnesium ion binding (GO:0000287), acetolactate synthase activity (GO:0003984), lyase activity (GO:0016829), thiamine pyrophosphate binding (GO:0030976), flavin adenine dinucleotide binding (GO:0050660), catalytic activity (GO:0003824), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), acetolactate synthase complex (GO:0005948), membrane (GO:0016020), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anion binding2
cation binding2
cytoplasm2
fatty acid catabolic process1
fatty acid oxidation1
pyruvate family amino acid biosynthetic process1
branched-chain amino acid biosynthetic process1
primary metabolic process1
lipid metabolic process1
monocarboxylic acid metabolic process1
metal ion binding1
transketolase or transaldolase activity1
catalytic activity1
vitamin binding1
quaternary ammonium group binding1
heterocyclic compound binding1
sulfur compound binding1
nucleotide binding1
molecular_function1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
transferase complex1
cellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2222 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HACL2SYDE1Q6ZW31538
HACL2EPHX3Q9H6B9527
HACL2LENG8Q96PV6480
HACL2XYLBO75191435
HACL2OR14A16Q8NHC5419
HACL2MYCP01106391
HACL2FHP07954390
HACL2HAO2Q9NYQ3390
HACL2PPCSQ9HAB8384
HACL2MYRFLQ96LU7379
HACL2TEKTL1Q8IYK2376
HACL2PSAT1Q9Y617376
HACL2H6PDO95479370
HACL2IARS1P41252360
HACL2SDSLQ96GA7357

IntAct

122 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
GBA2ILVBLpsi-mi:“MI:0914”(association)0.640
ILVBLCOG7psi-mi:“MI:0914”(association)0.640
COG7ILVBLpsi-mi:“MI:0914”(association)0.640
ILVBLCEP76psi-mi:“MI:0915”(physical association)0.560
PICK1ILVBLpsi-mi:“MI:0914”(association)0.530
ILKILVBLpsi-mi:“MI:0914”(association)0.530
DPEP1ILVBLpsi-mi:“MI:0914”(association)0.530
ILVBLEIF2B5psi-mi:“MI:0914”(association)0.530
ILVBLSLC33A1psi-mi:“MI:0914”(association)0.530
RHOBTB3ILVBLpsi-mi:“MI:0914”(association)0.530
SLC6A8ILVBLpsi-mi:“MI:0914”(association)0.530
ZMYM4ILVBLpsi-mi:“MI:0914”(association)0.530
FLT4ILVBLpsi-mi:“MI:0914”(association)0.420
COL14A1ILVBLpsi-mi:“MI:0915”(physical association)0.400
SDC1ILVBLpsi-mi:“MI:0915”(physical association)0.400
TOM1ILVBLpsi-mi:“MI:0915”(physical association)0.370
ATXN1ILVBLpsi-mi:“MI:0915”(physical association)0.370
Dctn3psi-mi:“MI:0914”(association)0.350
SKA1ILVBLpsi-mi:“MI:0914”(association)0.350

BioGRID (255): CEP76 (Two-hybrid), ILVBL (Affinity Capture-MS), ILVBL (Affinity Capture-MS), ATP1B1 (Co-fractionation), CYC1 (Co-fractionation), HSD17B14 (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), ILVBL (Co-fractionation), MTCH1 (Co-fractionation)

ESM2 similar proteins: A0A7J6EK66, A0A803PDZ0, A1L0T0, A2ATU0, A2XFI3, A2Y5L9, A2YQ76, A6QQT9, A7YWE4, O22567, O61856, O78328, O82647, P20906, P28516, P33287, P39994, P51845, P51846, P51850, P51851, P66947, P9WG38, P9WG39, Q0D3D2, Q0DHF6, Q0JMH0, Q10MW3, Q38854, Q3JAD1, Q3MHH6, Q3U4I7, Q4KLP0, Q5RAP5, Q68FT3, Q6DDK5, Q6JQN1, Q6NV04, Q6YU51, Q8BU33

Diamond homologs: A1L0T0, A6QQT9, O05031, O61856, P33287, P66947, P9WG38, P9WG39, Q58077, Q6DDK5, Q6NV04, Q8BU33, B9LNE4, A0A2I2F2I5, A4IPB6, B2TJ86, O06335, O08353, O19929, O33112, O78518, O85293, P00893, P07342, P08142, P09114, P09342, P0A623, P0AEP7, P0AEP8, P0DP89, P0DP90, P14874, P17597, P27696, P27818, P27819, P27868, P36620, P37063

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 113 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
SLC-mediated transmembrane transport96.2×7e-03

GO biological processes:

GO termPartnersFoldFDR
amino acid transport823.6×1e-06
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum515.9×7e-03
cell surface receptor protein tyrosine kinase signaling pathway69.8×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign12
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2493 predictions. Top by Δscore:

VariantEffectΔscore
19:15115427:TAAT:Tacceptor_gain1.0000
19:15115431:C:CCacceptor_gain1.0000
19:15115829:C:Adonor_gain1.0000
19:15115845:GTCAC:Gdonor_loss1.0000
19:15115846:TCAC:Tdonor_loss1.0000
19:15115847:CAC:Cdonor_loss1.0000
19:15115849:C:Tdonor_loss1.0000
19:15116145:T:TAdonor_gain1.0000
19:15116147:CTT:Cdonor_loss1.0000
19:15116148:TTA:Tdonor_loss1.0000
19:15116149:TA:Tdonor_loss1.0000
19:15116150:A:ACdonor_gain1.0000
19:15116150:A:AGdonor_loss1.0000
19:15116151:C:CCdonor_gain1.0000
19:15116227:C:CTdonor_gain1.0000
19:15116228:C:CTdonor_gain1.0000
19:15116318:CTCC:Cacceptor_gain1.0000
19:15116320:CC:Cacceptor_gain1.0000
19:15116321:CC:Cacceptor_gain1.0000
19:15116322:C:CCacceptor_gain1.0000
19:15116323:T:Aacceptor_loss1.0000
19:15116326:G:Tacceptor_gain1.0000
19:15117875:GCTCA:Gdonor_loss1.0000
19:15117876:CTCA:Cdonor_loss1.0000
19:15117877:TCA:Tdonor_loss1.0000
19:15117878:CAC:Cdonor_loss1.0000
19:15117879:A:ACdonor_gain1.0000
19:15117879:A:ATdonor_loss1.0000
19:15117879:AC:Adonor_gain1.0000
19:15117880:C:CCdonor_gain1.0000

AlphaMissense

4041 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:15123401:G:TA104D0.993
19:15115635:A:GW551R0.990
19:15115635:A:TW551R0.990
19:15115883:G:CS527R0.989
19:15115883:G:TS527R0.989
19:15115885:T:GS527R0.989
19:15123398:G:TA105D0.989
19:15116037:A:CF502L0.986
19:15116037:A:TF502L0.986
19:15116039:A:GF502L0.986
19:15123407:A:TV102D0.986
19:15115300:G:CN617K0.985
19:15115300:G:TN617K0.985
19:15116053:C:TG497E0.984
19:15116224:C:GD467H0.984
19:15123393:C:GA107P0.984
19:15116054:C:GG497R0.983
19:15116054:C:TG497R0.983
19:15120051:A:CF249L0.982
19:15120051:A:TF249L0.982
19:15120053:A:GF249L0.982
19:15123399:C:GA105P0.982
19:15123403:A:CF103L0.982
19:15123403:A:TF103L0.982
19:15123405:A:GF103L0.982
19:15123419:T:AE98V0.982
19:15123426:G:TR96S0.982
19:15116053:C:AG497V0.980
19:15117999:G:CF356L0.980
19:15117999:G:TF356L0.980

dbSNP variants (sampled 300 via entrez): RS1000164561 (19:15117713 A>G), RS1000201223 (19:15123460 G>A), RS1000820197 (19:15123301 G>A,C), RS1001052542 (19:15124542 C>G), RS1001483880 (19:15122704 T>C,G), RS1002326123 (19:15114621 C>A,G,T), RS1002732104 (19:15120946 C>T), RS1002823944 (19:15125824 G>A), RS1003230332 (19:15127328 A>G), RS1004486215 (19:15126527 A>G), RS1004843147 (19:15121383 T>C), RS1004953511 (19:15124201 G>C,T), RS1005005869 (19:15123950 G>A), RS1005266394 (19:15118876 C>A,T), RS1005294548 (19:15124249 G>A)

Disease associations

OMIM: gene MIM:605770 | 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
GCST000253_12Attention deficit hyperactivity disorder and conduct disorder8.000000e-06
GCST003771_20Loneliness8.000000e-07
GCST009391_646Metabolite levels9.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007865loneliness measurement
EFO:0010504inositol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066527 (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
5.00Kd1.004e+04nMCHEMBL5653589
5.00ED501.004e+04nMCHEMBL5653589

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
beta-Naphthoflavonedecreases expression2
bisphenol Fincreases expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
pirinixic acidaffects binding, increases activity, increases expression1
bisphenol Aincreases expression1
sodium arseniteincreases expression, increases abundance1
cobaltous chloridedecreases expression1
benzo(e)pyrenedecreases methylation1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
triacsin Cdecreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
bisphenol Bincreases expression1
bisphenol Sincreases expression1
jinfukangincreases expression1
LDN 193189affects cotreatment, increases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsincreases abundance, increases oxidation, affects cotreatment1
Arsenicincreases abundance, increases expression1
Cadmiumincreases expression, increases abundance1
Coumestrolincreases expression, affects cotreatment1
Estradiolincreases expression1
Hydrogen Peroxideincreases expression1
Ivermectindecreases expression1
Methapyrilenedecreases methylation1
Ozoneincreases abundance, affects cotreatment, increases oxidation1
Tunicamycinincreases expression1
Valproic Acidaffects expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651627BindingBinding affinity to human ILVBL 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.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): conduct disorder