HLCS

Summary

HLCS (holocarboxylase synthetase, HGNC:4976) is a protein-coding gene on chromosome 21q22.13, encoding Biotin–protein ligase (P50747). Biotin–protein ligase catalyzing the biotinylation of the 4 biotin-dependent carboxylases acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, and methylcrotonyl-CoA carboxylase.

This gene encodes an enzyme that catalyzes the binding of biotin to carboxylases and histones. The protein plays an important role in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. Defects in this gene are the cause of holocarboxylase synthetase deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 3141 — RefSeq curated summary.

At a glance

• Gene–disease (curated): holocarboxylase synthetase deficiency (Definitive, ClinGen)
• GWAS associations: 10
• Clinical variants (ClinVar): 1,133 total — 66 pathogenic, 102 likely-pathogenic
• Phenotypes (HPO): 34
• Druggable target: yes
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_001352514

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4976
Approved symbol	HLCS
Name	holocarboxylase synthetase
Location	21q22.13
Locus type	gene with protein product
Status	Approved
Aliases	HCS
Ensembl gene	ENSG00000159267
Ensembl biotype	protein_coding
OMIM	609018
Entrez	3141

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000336648, ENST00000399120, ENST00000427746, ENST00000448340, ENST00000482273, ENST00000612277, ENST00000674895, ENST00000675057, ENST00000675307, ENST00000876941

RefSeq mRNA: 8 — MANE Select: NM_001352514 NM_000411, NM_001242784, NM_001242785, NM_001352514, NM_001352515, NM_001352516, NM_001352517, NM_001352518

CCDS: CCDS13647, CCDS93094

Canonical transcript exons

ENST00000674895 — 11 exons

Exon	Start	End
ENSE00001044404	36930251	36930433
ENSE00001044408	36936449	36937392
ENSE00001108867	36759727	36759841
ENSE00001108868	36767218	36767285
ENSE00001108871	36756542	36756755
ENSE00001282128	36765012	36765172
ENSE00001282176	36896860	36897131
ENSE00001605772	36966444	36966669
ENSE00003902190	36748626	36754417
ENSE00003917719	36938832	36938994
ENSE00003920595	36962036	36962170

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 92.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5411 / max 61.2071, expressed in 1694 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
190378	3.2717	1490
190380	1.7467	1006
209309	0.4527	249
190379	0.0699	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
paraflocculus	UBERON:0005351	92.17	gold quality
frontal pole	UBERON:0002795	91.88	silver quality
middle frontal gyrus	UBERON:0002702	91.66	gold quality
buccal mucosa cell	CL:0002336	88.43	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.90	gold quality
stromal cell of endometrium	CL:0002255	81.51	gold quality
metanephros cortex	UBERON:0010533	81.38	gold quality
islet of Langerhans	UBERON:0000006	81.36	gold quality
parotid gland	UBERON:0001831	80.87	gold quality
lower esophagus mucosa	UBERON:0035834	79.77	gold quality
adrenal tissue	UBERON:0018303	79.55	gold quality
muscle of leg	UBERON:0001383	79.10	gold quality
right lobe of liver	UBERON:0001114	78.99	gold quality
gastrocnemius	UBERON:0001388	78.66	gold quality
pancreas	UBERON:0001264	78.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	78.16	gold quality
pituitary gland	UBERON:0000007	77.84	gold quality
adenohypophysis	UBERON:0002196	77.78	gold quality
ventricular zone	UBERON:0003053	77.62	gold quality
esophagus mucosa	UBERON:0002469	77.56	gold quality
endometrium epithelium	UBERON:0004811	77.55	silver quality
body of pancreas	UBERON:0001150	77.51	gold quality
corpus callosum	UBERON:0002336	77.43	gold quality
pancreatic ductal cell	CL:0002079	76.88	silver quality
tonsil	UBERON:0002372	76.81	gold quality
popliteal artery	UBERON:0002250	76.71	gold quality
tibial artery	UBERON:0007610	76.71	gold quality
right adrenal gland cortex	UBERON:0035827	76.63	gold quality
left adrenal gland	UBERON:0001234	76.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

161 targeting HLCS, 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-9-5P	100.00	72.28	2361
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3143	99.93	71.96	3104

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 28)

• 6 HLCS mutations were identified, including 2 new (N511K and G582R) and 4 known missense mutations (L216R, R508W, V550M, and G581S). 5 are in the biotin-binding domain. Tthe L216R change is in the N-terminal region outside the biotin-binding domain. (PMID:12124727)
• Detection of mutations by tandem mass spectrometry in Carnitine transporter deficiency. (PMID:17417720)
• findings from this study are consistent with the theory that HCS senses biotin, and that biotin regulates its own cellular uptake by participating in HCS-dependent chromatin remodeling events at the SMVT promoter 1 locus in Jurkat cells. (PMID:17904341)
• Study investigated cell lines from 2 HLCS-deficient patients p.L216R allele; enzyme activity was decreased for p.L216R and could not be increased by additional biotin; furthermore, the turn-over rate for the mutant protein was double that of wildtype. (PMID:18429047)
• Biotinylation of histones by BirA ligase is consistent with the proposed role of human HCS in chromatin. (PMID:18452652)
• The aim of this study was to investigate the effects of holocarboxylase synthetase (HCS) gene to irradiation in a time- and dose-dependent manner. (PMID:19048367)
• The hypothesis that N- and C-termini play roles in substrate recognition by HCS, was tested. (PMID:19157941)
• The mutations R508W and V363D of holocarboxylase synthetase might be hot-spots in Chinese children with holocarboxylase synthetas deficiency. (PMID:19695181)
• Amino termini of HCS influence biotin acceptor substrate recognition (PMID:19740736)
• 12 patients with multiple carboxylase deficiency, six mutations were found in the BT gene and 4 in the HLCS gene, including 5 novel mutations. (PMID:19806568)
• These results provide insights into substrate recognition by hHCS, which can be distinguished from BirA in this respect. (PMID:19914215)
• The study shows that not all the proteins and polypeptides that interact with holocarboxylase synthetase are targets for biotinylation, but that carboxylase- and histone-like structures are preferred HCS targets. (PMID:20026029)
• Data suggest that the N-terminal domain of hHCS recognizes the charged region of biotin acceptor protein, distinctly from the recognition by the catalytic domain. (PMID:20085763)
• Mutation analysis by polymerase chain reaction-sequencing of the entire coding region of the HLCS gene revealed the c.1522C>T (p.R508W) mutation in six of the eight mutant alleles. suggests it as the most common mutation in the Thai population (PMID:20095979)
• the localisation of HCS and its isoforms (PMID:20153287)
• The results of this study suggest that miR-539 is among the factors sensing biotin and regulating holocarboxylase synthetase expression. (PMID:20592104)
• Holocarboxylase synthetase interacts directly with histone H3, causing biotinylation of lysine K9 and K18. (PMID:20688500)
• HLCS methionine-58 is a functional translation start site in human cells. (PMID:21802411)
• individuals with HLCS SNPs may benefit from supplemental biotin, yet to different extents depending on the genotype (PMID:22027809)
• HLCS interacts physically with the DNA methyltransferase DNMT1 and the methyl CpG binding protein MeCP2 to facilitate the binding of HLCS to chromatin. (PMID:23624957)
• study characterizes three functional promoters in the human HLCS gene (PMID:24075901)
• This study showed that modification of HSP72 and demonstrated that binding of biotin to extracellular HSP72 prepares cells for a strong immune response. (PMID:24133061)
• The transcriptional function of HCS was shown by in vitro pull down and in vivo co-immunoprecipitation assays to depend on its interaction with the histone deacetylases HDAC1, HDAC2 and HDAC7 (PMID:24239178)
• Data suggest that direct interactions of HLCS (holocarboxylase synthetase) with NCOR1 (nuclear receptor corepressor 1) and HDAC1 (histone deacetylase 1) contribute toward transcriptional repression of repeats, presumably increasing genome stability. (PMID:24840043)
• The function of HCS and biotin in metabolism and human disease, a putative role for the enzyme in histone biotinylation, and its participation as a nuclear factor in chromatin dynamics is discussed. (PMID:28564555)
• Clinical, biochemical, and genetic analysis of 28 Chinese patients with holocarboxylase synthetase deficiency. (PMID:36890565)
• Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation. (PMID:37997490)
• CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis. (PMID:38493427)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	hlcs	ENSDARG00000039934
mus_musculus	Hlcs	ENSMUSG00000040820
rattus_norvegicus	Hlcs	ENSRNOG00000001686
drosophila_melanogaster	Hcs	FBGN0037332
caenorhabditis_elegans		WBGENE00000259

Protein

Protein identifiers

Biotin–protein ligase — P50747 (reviewed: P50747)

Alternative names: Biotin apo-protein ligase

All UniProt accessions (5): P50747, A0A0C4DG27, A0A6Q8PFK4, A0A8C8QSB1, C9JCQ9

UniProt curated annotations — full annotation on UniProt →

Function. Biotin–protein ligase catalyzing the biotinylation of the 4 biotin-dependent carboxylases acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, and methylcrotonyl-CoA carboxylase.

Subunit / interactions. Monomer.

Subcellular location. Cytoplasm. Mitochondrion.

Tissue specificity. Widely expressed. Mostly expressed in muscle, placenta and to a lower extent in the brain, kidney, pancreas, liver and lung.

Disease relevance. Holocarboxylase synthetase deficiency (HLCS deficiency) [MIM:253270] A neonatal form of multiple carboxylase deficiency, an autosomal recessive disorder of biotin metabolism, characterized by ketoacidosis, hyperammonemia, excretion of abnormal organic acid metabolites, and dermatitis. In holocarboxylase synthetase deficiency, clinical and biochemical symptoms improve dramatically with administration of biotin. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the biotin–protein ligase family.

Isoforms (2)

UniProt ID	Names	Canonical?
P50747-1	1	yes
P50747-2	2

RefSeq proteins (8): NP_000402, NP_001229713, NP_001229714, NP_001339443, NP_001339444, NP_001339445, NP_001339446, NP_001339447 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003142	BPL_C	Domain
IPR004143	BPL_LPL_catalytic	Domain
IPR004408	Biotin_CoA_COase_ligase	Family
IPR045864	aa-tRNA-synth_II/BPL/LPL	Homologous_superfamily

Pfam: PF02237, PF03099

Catalyzed reactions (Rhea), 4 shown:

• apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] + biotin + ATP = holo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] + AMP + diphosphate + H(+) (RHEA:11204)
• biotin + L-lysyl-[protein] + ATP = N(6)-biotinyl-L-lysyl-[protein] + AMP + diphosphate + H(+) (RHEA:11756)
• apo-[methylmalonyl-CoA:pyruvate carboxytransferase] + biotin + ATP = holo-[methylmalonyl-CoA:pyruvate carboxytransferase] + AMP + diphosphate + H(+) (RHEA:23668)
• apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] + biotin + ATP = holo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] + AMP + diphosphate + H(+) (RHEA:24376)

UniProt features (35 total): sequence variant 25, sequence conflict 3, modified residue 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P50747-F1	77.33	0.44

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 (2): 147, 299

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-196780	Biotin transport and metabolism
R-HSA-3371599	Defective HLCS causes multiple carboxylase deficiency
R-HSA-1430728	Metabolism
R-HSA-1643685	Disease
R-HSA-196849	Metabolism of water-soluble vitamins and cofactors
R-HSA-196854	Metabolism of vitamins and cofactors
R-HSA-3296482	Defects in vitamin and cofactor metabolism
R-HSA-3323169	Defects in biotin (Btn) metabolism
R-HSA-5668914	Diseases of metabolism

MSigDB gene sets: 234 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, CTATGCA_MIR153, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOMF_LIGASE_ACTIVITY_FORMING_CARBON_NITROGEN_BONDS, CHO_NR4A1_TARGETS, GOBP_RESPONSE_TO_VITAMIN, HUANG_FOXA2_TARGETS_UP, chr21q22, GOBP_RESPONSE_TO_NUTRIENT

GO Biological Process (4): biotin metabolic process (GO:0006768), post-translational protein modification (GO:0043687), response to biotin (GO:0070781), protein modification process (GO:0036211)

GO Molecular Function (9): biotin–[biotin carboxyl-carrier protein] ligase activity (GO:0004077), ATP binding (GO:0005524), biotin binding (GO:0009374), enzyme binding (GO:0019899), identical protein binding (GO:0042802), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), ligase activity (GO:0016874)

GO Cellular Component (6): chromatin (GO:0000785), nuclear lamina (GO:0005652), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829), nuclear matrix (GO:0016363)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Metabolism of water-soluble vitamins and cofactors	1
Defects in biotin (Btn) metabolism	1
Metabolism of vitamins and cofactors	1
Metabolism	1
Diseases of metabolism	1
Defects in vitamin and cofactor metabolism	1
Disease	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
heterocyclic compound binding	2
protein binding	2
cytoplasm	2
sulfur compound metabolic process	1
monocarboxylic acid metabolic process	1
protein modification process	1
response to vitamin	1
response to nitrogen compound	1
response to oxygen-containing compound	1
protein metabolic process	1
macromolecule modification	1
ligase activity, forming carbon-nitrogen bonds	1
catalytic activity, acting on a protein	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
vitamin binding	1
monocarboxylic acid binding	1
sulfur compound binding	1
nucleoside phosphate binding	1
molecular_function	1
binding	1
catalytic activity	1
chromosome	1
nuclear envelope	1
nuclear periphery	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Protein interactions and networks

STRING

2454 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HLCS	BTD	P43251	968
HLCS	PC	P11498	964
HLCS	MCCC1	Q96RQ3	934
HLCS	PCCA	P05165	923
HLCS	ACACA	Q13085	821
HLCS	EHMT1	Q9H9B1	651
HLCS	SLC5A6	Q9Y289	625
HLCS	MCCC2	Q9HCC0	606
HLCS	PCCB	P05166	593
HLCS	MECP2	P51608	538
HLCS	KCNJ6	P48051	521
HLCS	MOCS1	Q9NZB8	518
HLCS	DNMT1	P26358	505
HLCS	ACACB	O00763	496
HLCS	OXSM	Q9NWU1	448

IntAct

48 interactions, top by confidence:

A	B	Type	Score
HLCS	SPATA46	psi-mi:“MI:0915”(physical association)	0.740
HLCS	ACACB	psi-mi:“MI:0414”(enzymatic reaction)	0.620
HLCS	ACACB	psi-mi:“MI:0407”(direct interaction)	0.620
CATSPERD	HLCS	psi-mi:“MI:0915”(physical association)	0.590
HLCS	ANKRD29	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-9	HLCS	psi-mi:“MI:0915”(physical association)	0.560
MED19	HLCS	psi-mi:“MI:0915”(physical association)	0.560
SPATA46	TYW5	psi-mi:“MI:0914”(association)	0.530
TMC7	HLCS	psi-mi:“MI:0914”(association)	0.530
SPATA46	MDM4	psi-mi:“MI:0914”(association)	0.530
POT1	HLCS	psi-mi:“MI:0915”(physical association)	0.510
HLCS	HLCS	psi-mi:“MI:0407”(direct interaction)	0.440
PTP4A1	PSMD3	psi-mi:“MI:0914”(association)	0.420
PTP4A1	PSMD3	psi-mi:“MI:2364”(proximity)	0.420
HLCS	THOC2	psi-mi:“MI:0915”(physical association)	0.400
HLCS	MYH7B	psi-mi:“MI:0915”(physical association)	0.400
HLCS	TBC1D20	psi-mi:“MI:0915”(physical association)	0.400
HLCS	DDX52	psi-mi:“MI:0915”(physical association)	0.370
HLCS	SNX27	psi-mi:“MI:0915”(physical association)	0.370
CDKN3	STMN1	psi-mi:“MI:0914”(association)	0.350
DUSP15	PSMD3	psi-mi:“MI:0914”(association)	0.350
DUSP22	ACACB	psi-mi:“MI:0914”(association)	0.350
RAB9A	LANCL1	psi-mi:“MI:0914”(association)	0.350
TMC7	PSMD11	psi-mi:“MI:0914”(association)	0.350
CD63	ABCC4	psi-mi:“MI:0914”(association)	0.350

BioGRID (52): HLCS (Affinity Capture-MS), HLCS (Affinity Capture-MS), HLCS (Affinity Capture-MS), TBC1D20 (Affinity Capture-MS), HLCS (Affinity Capture-MS), HLCS (Affinity Capture-MS), HLCS (Affinity Capture-MS), HLCS (Affinity Capture-MS), HLCS (Affinity Capture-MS), HLCS (Proximity Label-MS), HLCS (Affinity Capture-MS), HLCS (Affinity Capture-RNA), HLCS (Affinity Capture-MS), HLCS (Proximity Label-MS), HLCS (Proximity Label-MS)

ESM2 similar proteins: A0A0D3QS98, A0A0D3QS99, A4D0V7, C5H5C4, F6Q1T7, O70309, O75354, P17405, P18084, P18424, P22413, P50747, P52850, P58242, P61642, P80747, Q04519, Q0VBD0, Q0VD19, Q13219, Q52KP5, Q58CQ9, Q5QQ51, Q5STE3, Q64687, Q6DFZ6, Q6KFX9, Q6MZW2, Q6P988, Q6UWX4, Q6YGZ1, Q6ZXD2, Q71RP1, Q812F8, Q8BJQ9, Q8C1F4, Q8C419, Q8N5D6, Q8N6G5, Q8R116

Diamond homologs: E0U174, F4I4W2, O14353, P06709, P0CI75, P29906, P37416, P50747, Q5F5C8, Q920N2, Q9JWI7, Q9JXF1, Q9SL92, I6YFP0, P46363, Q59014

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1133 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	66
Likely pathogenic	102
Uncertain significance	324
Likely benign	446
Benign	68

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1071012	NC_000021.8:g.(?38269140)(38269451_?)del	Pathogenic
1071507	NC_000021.8:g.(?38302541)(38311304_?)del	Pathogenic
1071508	NC_000021.8:g.(?38269140)(38311203_?)del	Pathogenic
1075159	NM_001352514.2(HLCS):c.1156C>T (p.Gln386Ter)	Pathogenic
1413934	NM_001352514.2(HLCS):c.2361_2362insT (p.Val788fs)	Pathogenic
1452545	NM_001352514.2(HLCS):c.1634del (p.Pro545fs)	Pathogenic
1452913	NM_001352514.2(HLCS):c.1627_1628del (p.Arg543fs)	Pathogenic
1454873	NM_001352514.2(HLCS):c.763G>T (p.Glu255Ter)	Pathogenic
1457493	NC_000021.8:g.(?38132018)(38362704_?)del	Pathogenic
1458476	NM_001352514.2(HLCS):c.1543del (p.Ile514_Leu515insTer)	Pathogenic
1460039	NM_001352514.2(HLCS):c.727del (p.Val243fs)	Pathogenic
1685876	NM_001352514.2(HLCS):c.2279T>C (p.Ile760Thr)	Pathogenic
1907	NM_001352514.2(HLCS):c.1151T>C (p.Leu384Pro)	Pathogenic
1912	NM_001352514.2(HLCS):c.1960+5G>A	Pathogenic
1913	NM_001352514.2(HLCS):c.1096dup (p.Ile366fs)	Pathogenic
1962881	NM_001352514.2(HLCS):c.2458del (p.Gln820fs)	Pathogenic
199017	NM_001352514.2(HLCS):c.2065C>T (p.Gln689Ter)	Pathogenic
1996544	NM_001352514.2(HLCS):c.1444_1456delinsATAGTGCAAACTCCAACATAGTGCAAACT (p.Leu482_Pro486delinsIleValGlnThrProThrTer)	Pathogenic
1998913	NM_001352514.2(HLCS):c.2301C>G (p.Tyr767Ter)	Pathogenic
2013320	NM_001352514.2(HLCS):c.1831C>T (p.Gln611Ter)	Pathogenic
203775	NM_001352514.2(HLCS):c.2333del (p.Pro777_Leu778insTer)	Pathogenic
203777	NM_001352514.2(HLCS):c.1223del (p.Gly408fs)	Pathogenic
2045052	NM_001352514.2(HLCS):c.2439C>G (p.Tyr813Ter)	Pathogenic
2087682	NM_001352514.2(HLCS):c.2128_2135delinsTAAAGGGTGA (p.Asn710_Arg712delinsTer)	Pathogenic
2092902	NM_001352514.2(HLCS):c.1631dup (p.Asp544fs)	Pathogenic
2124510	NM_001352514.2(HLCS):c.2212_2213del (p.Gly738fs)	Pathogenic
2153897	NM_001352514.2(HLCS):c.1599_1600del (p.Tyr534fs)	Pathogenic
2178678	NM_001352514.2(HLCS):c.1799T>G (p.Leu600Ter)	Pathogenic
2228569	NM_001352514.2(HLCS):c.2140A>T (p.Lys714Ter)	Pathogenic
235250	NM_001352514.2(HLCS):c.2446C>T (p.His816Tyr)	Pathogenic

SpliceAI

4692 predictions. Top by Δscore:

Variant	Effect	Δscore
21:36754415:CCA:C	acceptor_gain	1.0000
21:36754416:CA:C	acceptor_gain	1.0000
21:36754416:CAC:C	acceptor_gain	1.0000
21:36754418:C:CC	acceptor_gain	1.0000
21:36756852:T:TA	donor_gain	1.0000
21:36767213:CTGA:C	donor_loss	1.0000
21:36767214:TGA:T	donor_loss	1.0000
21:36767215:GA:G	donor_loss	1.0000
21:36767216:ACCTT:A	donor_loss	1.0000
21:36767217:CCTTT:C	donor_loss	1.0000
21:36896912:T:A	donor_gain	1.0000
21:36930243:CAACT:C	donor_loss	1.0000
21:36930244:AACTC:A	donor_loss	1.0000
21:36930245:ACTCA:A	donor_loss	1.0000
21:36930246:CTCA:C	donor_loss	1.0000
21:36930247:TCAC:T	donor_loss	1.0000
21:36930248:CA:C	donor_loss	1.0000
21:36930250:C:CT	donor_loss	1.0000
21:36936502:T:TA	donor_gain	1.0000
21:36937388:CACCG:C	acceptor_gain	1.0000
21:36937393:C:CC	acceptor_gain	1.0000
21:36937399:C:CT	acceptor_gain	1.0000
21:36937400:A:C	acceptor_gain	1.0000
21:36937400:A:T	acceptor_gain	1.0000
21:36937404:A:AC	acceptor_gain	1.0000
21:36938830:A:AC	donor_gain	1.0000
21:36938831:C:CC	donor_gain	1.0000
21:36938831:CA:C	donor_gain	1.0000
21:36938831:CACA:C	donor_gain	1.0000
21:36938835:CAAT:C	donor_gain	1.0000

AlphaMissense

5711 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:36759820:A:G	W568R	1.000
21:36759820:A:T	W568R	1.000
21:36759818:C:A	W568C	0.998
21:36759818:C:G	W568C	0.998
21:36759810:T:A	D571V	0.997
21:36759810:T:G	D571A	0.996
21:36759821:C:A	K567N	0.996
21:36759821:C:G	K567N	0.996
21:36759823:T:C	K567E	0.996
21:36754343:A:T	L695H	0.995
21:36759809:A:C	D571E	0.995
21:36759809:A:T	D571E	0.995
21:36759810:T:C	D571G	0.994
21:36754343:A:G	L695P	0.993
21:36756552:A:G	W667R	0.993
21:36756552:A:T	W667R	0.993
21:36759811:C:G	D571H	0.993
21:36759812:G:C	N570K	0.993
21:36759812:G:T	N570K	0.993
21:36765038:C:G	A552P	0.993
21:36765147:G:C	S515R	0.993
21:36765147:G:T	S515R	0.993
21:36765149:T:G	S515R	0.993
21:36759816:G:T	P569H	0.992
21:36759819:C:G	W568S	0.992
21:36765049:G:T	A548D	0.992
21:36765061:A:G	L544P	0.992
21:36765155:A:G	W513R	0.991
21:36765155:A:T	W513R	0.991
21:36759785:C:A	K579N	0.990

dbSNP variants (sampled 300 via entrez): RS1000014263 (21:36923001 C>T), RS1000018370 (21:36817648 C>A,T), RS1000019247 (21:36843264 C>A), RS1000020975 (21:36766497 T>C), RS1000027422 (21:36903065 G>C,T), RS1000058351 (21:36896827 C>G), RS1000068343 (21:36934114 C>G,T), RS1000069746 (21:36893540 G>A), RS1000074757 (21:36847036 A>T), RS1000080455 (21:36770747 T>C), RS1000087647 (21:36886901 A>G), RS1000122239 (21:36790848 G>T), RS1000129663 (21:36847408 T>C), RS1000140792 (21:36839204 G>A), RS1000152314 (21:36858908 G>A)

Disease associations

OMIM: gene MIM:609018 | disease phenotypes: MIM:253270, MIM:277460

GenCC curated gene-disease

Disease	Classification	Inheritance
holocarboxylase synthetase deficiency	Definitive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
holocarboxylase synthetase deficiency	Definitive	AR

Mondo (2): holocarboxylase synthetase deficiency (MONDO:0009666), familial isolated deficiency of vitamin E (MONDO:0010188)

Orphanet (2): Holocarboxylase synthetase deficiency (Orphanet:79242), Ataxia with vitamin E deficiency (Orphanet:96)

HPO phenotypes

34 total (30 of 34 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000737	Irritability
HP:0000964	Eczematoid dermatitis
HP:0000988	Skin rash
HP:0001096	Keratoconjunctivitis
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001254	Lethargy
HP:0001259	Coma
HP:0001263	Global developmental delay
HP:0001276	Hypertonia
HP:0001290	Generalized hypotonia
HP:0001510	Growth delay
HP:0001596	Alopecia
HP:0001824	Weight loss
HP:0001873	Thrombocytopenia
HP:0001942	Metabolic acidosis
HP:0001987	Hyperammonemia
HP:0001992	Organic aciduria
HP:0002013	Vomiting
HP:0002017	Nausea and vomiting
HP:0002039	Anorexia
HP:0002098	Respiratory distress
HP:0002789	Tachypnea
HP:0002883	Hyperventilation
HP:0003128	Lactic acidosis
HP:0003623	Neonatal onset
HP:0007549	Desquamation of skin soon after birth
HP:0008872	Feeding difficulties in infancy

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST003396_4	Developmental language disorder	5.000000e-06
GCST003397_1	Developmental language disorder (linguistic errors)	5.000000e-07
GCST003397_5	Developmental language disorder (linguistic errors)	2.000000e-07
GCST003542_70	Night sleep phenotypes	1.000000e-06
GCST005576_10	Intracranial aneurysm	5.000000e-07
GCST007102_16	Seasonality and depression	4.000000e-06
GCST90002383_322	Hematocrit	3.000000e-10
GCST90002383_323	Hematocrit	2.000000e-14
GCST90002384_491	Hemoglobin	2.000000e-11
GCST90002403_543	Red blood cell count	6.000000e-10

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007798	linguistic error measurement
EFO:0007827	nighttime rest measurement
EFO:0006876	seasonality measurement
EFO:0004348	hematocrit
EFO:0004509	hemoglobin measurement
EFO:0004305	erythrocyte count

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D028922	Holocarboxylase Synthetase Deficiency	C16.320.565.100.620.380; C16.320.565.202.720.380; C18.452.648.100.620.380; C18.452.648.202.720.380
C535393	Ataxia with vitamin E deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2062354 (SINGLE PROTEIN)

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

ChEMBL bioactivities

8 potent at pChembl≥5 of 11 total, top 8 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.85	Ki	140	nM	CHEMBL2063402
6.74	Ki	182	nM	CHEMBL1231498
6.70	Ki	200	nM	CHEMBL2063403
5.70	Ki	2000	nM	CHEMBL3357333
5.46	Ki	3500	nM	CHEMBL2063404
5.42	Ki	3850	nM	CHEMBL2063398
5.19	Ki	6430	nM	CHEMBL2062535
5.06	IC50	8800	nM	CHEMBL1231498

PubChem BioAssay actives

8 with measured affinity, of 74 total; 7 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(3aS,4S,6aR)-4-pentyl-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-2-one	674012: Displacement of [3H]-biotin from human BPL after 20 mins by scintillation counting	ki	0.1400	uM
5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentyl [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl hydrogen phosphate	1203013: Inhibition of human recombinant BPL using 3H-biotin as substrate after 10 mins by liquid scintillation counting analysis	ki	0.1820	uM
(3aS,4S,6aR)-4-hex-5-ynyl-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-2-one	674012: Displacement of [3H]-biotin from human BPL after 20 mins by scintillation counting	ki	0.2000	uM
[6-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]-2-oxohexyl]-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy]phosphinic acid;azane	1175012: Inhibition of human recombinant HLCS using P67 as substrate after 2 hrs relative to vehicle-treated control	ki	2.0000	uM
(3aS,4S,6aR)-4-hept-6-ynyl-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-2-one	674012: Displacement of [3H]-biotin from human BPL after 20 mins by scintillation counting	ki	3.5000	uM
(3aS,4S,6aR)-4-(5-hydroxypentyl)-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-2-one	674012: Displacement of [3H]-biotin from human BPL after 20 mins by scintillation counting	ki	3.8500	uM
(3aS,4S,6aR)-4-hexyl-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-2-one	674012: Displacement of [3H]-biotin from human BPL after 20 mins by scintillation counting	ki	6.4300	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	5
Aflatoxin B1	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
FR900359	affects phosphorylation	1
ferulic acid	decreases activity	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
trichostatin A	increases expression, decreases reaction	1
cyanidin	decreases activity	1
sodium arsenite	affects methylation	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	decreases phosphorylation	1
fumaric acid	decreases activity	1
3-hydroxybenzoic acid	decreases activity	1
4-hydroxybenzoic acid	decreases activity	1
2,3,4,5-tetrachlorophenate	affects response to substance	1
caffeic acid	decreases activity	1
3,3’,4,5’-tetrahydroxystilbene	decreases activity	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
polydatin	decreases activity	1
chromium hexavalent ion	affects expression, increases expression, increases reaction, decreases reaction	1
CGP 52608	affects binding, increases reaction	1
p-coumaric acid	decreases activity	1
Resveratrol	decreases activity	1
Decitabine	increases expression, increases reaction	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Ascorbic Acid	decreases activity	1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL2065962	Binding	Displacement of [3H]-biotin from human BPL after 20 mins by scintillation counting	Biotin analogues with antibacterial activity are potent inhibitors of biotin protein ligase. — ACS Med Chem Lett

Cellosaurus cell lines

4 cell lines: 2 finite cell line, 1 induced pluripotent stem cell, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A3ZB	DS-1-iPSC	Induced pluripotent stem cell	Female
CVCL_E0EA	Ubigene HeLa HLCS KO	Cancer cell line	Female
CVCL_H551	GM11576	Finite cell line	Female
CVCL_W010	GM10309	Finite cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03655223	Not specified	ENROLLING_BY_INVITATION	Early Check: Expanded Screening in Newborns
NCT05687474	Not specified	COMPLETED	Baby Detect : Genomic Newborn Screening
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford