PPCS

gene
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Also known as FLJ11838

Summary

PPCS (phosphopantothenoylcysteine synthetase, HGNC:25686) is a protein-coding gene on chromosome 1p34.2, encoding Phosphopantothenate–cysteine ligase (Q9HAB8). Catalyzes the second step in the biosynthesis of coenzyme A from vitamin B5, where cysteine is conjugated to 4’-phosphopantothenate to form 4-phosphopantothenoylcysteine. It is a selective cancer dependency (DepMap: 16.6% of cell lines).

Biosynthesis of coenzyme A (CoA) from pantothenic acid (vitamin B5) is an essential universal pathway in prokaryotes and eukaryotes. PPCS (EC 6.3.2.5), one of the last enzymes in this pathway, converts phosphopantothenate to phosphopantothenoylcysteine (Daugherty et al., 2002 [PubMed 11923312]).

Source: NCBI Gene 79717 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cardiomyopathy, dilated, 2c (Strong, GenCC) — +1 more curated relationship
  • Clinical variants (ClinVar): 40 total
  • Phenotypes (HPO): 23
  • Cancer dependency (DepMap): dependent in 16.6% of screened cell lines
  • MANE Select transcript: NM_024664

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25686
Approved symbolPPCS
Namephosphopantothenoylcysteine synthetase
Location1p34.2
Locus typegene with protein product
StatusApproved
AliasesFLJ11838
Ensembl geneENSG00000127125
Ensembl biotypeprotein_coding
OMIM609853
Entrez79717

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000372556, ENST00000372560, ENST00000372561, ENST00000372562, ENST00000469615, ENST00000471420, ENST00000472013, ENST00000482168, ENST00000933676

RefSeq mRNA: 7 — MANE Select: NM_024664 NM_001077447, NM_001287506, NM_001287508, NM_001287509, NM_001287510, NM_001287511, NM_024664

CCDS: CCDS41311, CCDS41312

Canonical transcript exons

ENST00000372561 — 3 exons

ExonStartEnd
ENSE000019015764245654342457073
ENSE000035193054245960342461236
ENSE000036456154245724742457350

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 97.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 38.4210 / max 287.8256, expressed in 1824 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
245738.42101824

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right adrenal gland cortexUBERON:003582797.05gold quality
body of pancreasUBERON:000115097.04gold quality
right adrenal glandUBERON:000123396.91gold quality
calcaneal tendonUBERON:000370196.88gold quality
rectumUBERON:000105296.82gold quality
mucosa of transverse colonUBERON:000499196.70gold quality
monocyteCL:000057696.61gold quality
mononuclear cellCL:000084296.49gold quality
leukocyteCL:000073896.44gold quality
left adrenal glandUBERON:000123496.38gold quality
left adrenal gland cortexUBERON:003582596.16gold quality
adrenal tissueUBERON:001830396.04gold quality
body of stomachUBERON:000116196.02gold quality
metanephros cortexUBERON:001053396.02gold quality
gall bladderUBERON:000211095.98gold quality
tendonUBERON:000004395.79gold quality
transverse colonUBERON:000115795.79gold quality
minor salivary glandUBERON:000183095.72gold quality
right coronary arteryUBERON:000162595.47gold quality
small intestine Peyer’s patchUBERON:000345495.41gold quality
pancreasUBERON:000126495.39gold quality
granulocyteCL:000009495.35gold quality
adrenal cortexUBERON:000123595.35gold quality
adrenal glandUBERON:000236995.33gold quality
olfactory segment of nasal mucosaUBERON:000538695.30gold quality
saliva-secreting glandUBERON:000104495.25gold quality
skin of abdomenUBERON:000141695.04gold quality
adult mammalian kidneyUBERON:000008295.00gold quality
left coronary arteryUBERON:000162694.96gold quality
esophagus mucosaUBERON:000246994.90gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-CURD-10no496.16
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting PPCS, 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-340-5P100.0072.504437
HSA-MIR-574-5P100.0066.01989
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-60799.9773.625593
HSA-MIR-50799.9770.111915
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-9-3P99.9670.882068
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-806399.9169.763146
HSA-MIR-129-5P99.8870.263273
HSA-MIR-137-3P99.8774.742401
HSA-MIR-469899.8471.414303
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-489-3P99.8066.46839
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-320A-3P99.7769.732107
HSA-MIR-320B99.7769.732107
HSA-MIR-320C99.7769.732107
HSA-MIR-320D99.7769.732107
HSA-MIR-442999.7769.622111
HSA-MIR-7856-5P99.7569.992901

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 16.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Oxygen transfer studies found that 18O from [carboxyl-18O] phosphopantothenate is incorporated into AMP or CMP produced during PPCS catalysis, consistent with the formation of a phosphopantothenoyl cytidylate or phosphopantothenoyl adenylate intermediate (PMID:19683078)
  • Exome sequencing in five individuals from two unrelated families presenting with dilated cardiomyopathy revealed biallelic mutations in PPCS. (PMID:29754768)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioppcsENSDARG00000061889
mus_musculusPpcsENSMUSG00000028636
rattus_norvegicusPpcsENSRNOG00000008572
drosophila_melanogasterPpcsFBGN0261285
caenorhabditis_elegansWBGENE00022171

Paralogs (4): CNIH1 (ENSG00000100528), CNIH4 (ENSG00000143771), CNIH3 (ENSG00000143786), CNIH2 (ENSG00000174871)

Protein

Protein identifiers

Phosphopantothenate–cysteine ligaseQ9HAB8 (reviewed: Q9HAB8)

Alternative names: Phosphopantothenoylcysteine synthetase

All UniProt accessions (3): Q9HAB8, Q5VVM2, Q5VVM3

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the second step in the biosynthesis of coenzyme A from vitamin B5, where cysteine is conjugated to 4’-phosphopantothenate to form 4-phosphopantothenoylcysteine. Has a preference for ATP over CTP as a cosubstrate.

Subunit / interactions. Homodimer.

Disease relevance. Cardiomyopathy, dilated, 2C (CMD2C) [MIM:618189] A form of dilated cardiomyopathy, a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. CMD2C is an autosomal recessive form with variable severity and age of onset ranging from 2 to 20 years. Death in infancy or early childhood may occur in severely affected children. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 2/5.

Similarity. Belongs to the PPC synthetase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9HAB8-11yes
Q9HAB8-22

RefSeq proteins (7): NP_001070915, NP_001274435, NP_001274437, NP_001274438, NP_001274439, NP_001274440, NP_078940* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007085DNA/pantothenate-metab_flavo_CDomain
IPR035929CoaB-like_sfHomologous_superfamily

Pfam: PF04127

Enzyme classification (BRENDA):

  • EC 6.3.2.51 — phosphopantothenate-cysteine ligase (ATP) (BRENDA: 9 organisms, 9 substrates, 8 inhibitors, 9 Km, 5 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
(R)-4’-PHOSPHOPANTOTHENATE0.013–0.0573
L-CYSTEINE0.014–0.0863
CTP0.156–0.2652
ATP0.2691

Catalyzed reactions (Rhea), 2 shown:

  • (R)-4’-phosphopantothenate + L-cysteine + CTP = N-[(R)-4-phosphopantothenoyl]-L-cysteine + CMP + diphosphate + H(+) (RHEA:19397)
  • (R)-4’-phosphopantothenate + L-cysteine + ATP = N-[(R)-4-phosphopantothenoyl]-L-cysteine + AMP + diphosphate + H(+) (RHEA:25156)

UniProt features (38 total): helix 15, strand 14, sequence variant 3, turn 2, initiator methionine 1, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
7EDZX-RAY DIFFRACTION1.95
1P9OX-RAY DIFFRACTION2.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HAB8-F193.940.85

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-196783Coenzyme A biosynthesis

MSigDB gene sets: 179 (showing top): FXR_IR1_Q6, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_COENZYME_A_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_ACETYL_COA_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_SULFUR_COMPOUND_BIOSYNTHETIC_PROCESS, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_AMIDE_BIOSYNTHETIC_PROCESS, USF_01, chr1p34

GO Biological Process (3): heart process (GO:0003015), acetyl-CoA biosynthetic process (GO:0006085), coenzyme A biosynthetic process (GO:0015937)

GO Molecular Function (7): phosphopantothenate–cysteine ligase activity (GO:0004632), ATP binding (GO:0005524), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), ligase activity (GO:0016874)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Vitamin B5 (pantothenate) metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
circulatory system process1
acetyl-CoA metabolic process1
acyl-CoA biosynthetic process1
coenzyme A metabolic process1
sulfur compound biosynthetic process1
purine-containing compound biosynthetic process1
nucleoside phosphate biosynthetic process1
acid-amino acid ligase activity1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
protein binding1
identical protein binding1
protein dimerization activity1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

862 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PPCSPPCDCQ96CD2957
PPCSCOASYQ13057932
PPCSPANK1Q8TE04756
PPCSPANK2Q9BZ23710
PPCSPANK3Q9H999697
PPCSPANK4Q9NVE7639
PPCSDCAKDQ8WVC6502
PPCSPPANQ9NQ55478
PPCSGOLPH3Q9H4A6399
PPCSDUX4L2P0CJ85399
PPCSHACL2A1L0T0384
PPCSRBM14Q96PK6377
PPCSA0A0B4J1V8A0A0B4J1V8355
PPCSNUDT8Q8WV74344
PPCSSLC25A42Q86VD7329

IntAct

21 interactions, top by confidence:

ABTypeScore
C5orf46TMBIM6psi-mi:“MI:0914”(association)0.560
PPCSPPCSpsi-mi:“MI:0915”(physical association)0.560
FBXO16CETN3psi-mi:“MI:0914”(association)0.530
TRMT44PPCSpsi-mi:“MI:0915”(physical association)0.400
PPCSCLOCKpsi-mi:“MI:0915”(physical association)0.400
BST1GXYLT2psi-mi:“MI:0914”(association)0.350
PPCSSCGB2A1psi-mi:“MI:0914”(association)0.350
GXYLT2HSPA8psi-mi:“MI:0914”(association)0.350
CCR1UBA6psi-mi:“MI:0914”(association)0.350
SPRED2SMCHD1psi-mi:“MI:0914”(association)0.350
MPIADApsi-mi:“MI:0914”(association)0.350
PNPLA4PCCApsi-mi:“MI:0914”(association)0.350
GAB2UBA6psi-mi:“MI:0914”(association)0.350
MARS2DDX39Apsi-mi:“MI:0914”(association)0.350
NPPBACOT7psi-mi:“MI:0914”(association)0.350
VENTXUBA6psi-mi:“MI:0914”(association)0.350
SLC13A4POLR3Apsi-mi:“MI:0914”(association)0.350
PPCSPPCSpsi-mi:“MI:0915”(physical association)0.000
PPCSpsi-mi:“MI:0915”(physical association)0.000

BioGRID (67): PPCS (Co-fractionation), PPCS (Co-fractionation), PPCS (Affinity Capture-MS), PPCS (Negative Genetic), PPCS (Positive Genetic), PPCS (Positive Genetic), PPCS (Positive Genetic), PPCS (Positive Genetic), PPCS (Positive Genetic), PPCS (Negative Genetic), PPCS (Positive Genetic), PPCS (Negative Genetic), PPCS (Positive Genetic), PPCS (Negative Genetic), PPCS (Positive Genetic)

ESM2 similar proteins: A0A7N9VSG0, A0JNU3, D3ZBP4, D3ZX08, F1MH07, O43542, O55137, O55171, O88202, O88267, P15575, P16444, P22412, P31429, P41226, P43477, Q08DH8, Q0P5I5, Q14CH7, Q2KHY1, Q2V057, Q32Q92, Q3SZM7, Q3UQ84, Q5E9L5, Q5JTZ9, Q5M876, Q5RCH4, Q66KF6, Q68FW7, Q6P3H4, Q6PAY6, Q86U10, Q8K4F6, Q8K4V2, Q8R123, Q8TDZ2, Q8VCZ9, Q8VDG5, Q8VDP3

Diamond homologs: P40506, Q0J7N5, Q69S81, Q8GXR5, Q8VDG5, Q9HAB8, Q9LZM3, Q9USK7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance14
Likely benign21
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

357 predictions. Top by Δscore:

VariantEffectΔscore
1:42457241:TTGCA:Tacceptor_loss1.0000
1:42457242:TGCA:Tacceptor_loss1.0000
1:42457243:GCA:Gacceptor_loss1.0000
1:42457244:CAGGC:Cacceptor_loss1.0000
1:42457245:A:AGacceptor_gain1.0000
1:42457245:A:Cacceptor_loss1.0000
1:42457246:G:GGacceptor_gain1.0000
1:42457006:AG:Adonor_gain0.9900
1:42457069:GCTAG:Gdonor_gain0.9900
1:42457070:C:Gdonor_gain0.9900
1:42457070:CTAGG:Cdonor_loss0.9900
1:42457071:TAGGT:Tdonor_loss0.9900
1:42457072:AGGTG:Adonor_loss0.9900
1:42457073:GGTG:Gdonor_loss0.9900
1:42457074:G:Tdonor_loss0.9900
1:42457075:T:Adonor_loss0.9900
1:42457245:AG:Aacceptor_gain0.9900
1:42457246:GG:Gacceptor_gain0.9900
1:42457246:GGC:Gacceptor_gain0.9900
1:42457246:GGCC:Gacceptor_gain0.9900
1:42457246:GGCCC:Gacceptor_gain0.9900
1:42457105:G:GTdonor_gain0.9800
1:42456974:G:GTdonor_gain0.9700
1:42457346:TGCAG:Tdonor_loss0.9700
1:42457347:GCAGG:Gdonor_loss0.9700
1:42457348:CAGGT:Cdonor_loss0.9700
1:42457349:AGG:Adonor_loss0.9700
1:42457350:GGT:Gdonor_loss0.9700
1:42457351:GTG:Gdonor_loss0.9700
1:42457352:T:Adonor_loss0.9700

AlphaMissense

1986 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:42457010:T:CF149L0.997
1:42457012:C:AF149L0.997
1:42457012:C:GF149L0.997
1:42456742:C:AN59K0.996
1:42456742:C:GN59K0.996
1:42459678:T:CF230L0.994
1:42459680:T:AF230L0.994
1:42459680:T:GF230L0.994
1:42456746:A:CS61R0.993
1:42456748:C:AS61R0.993
1:42456748:C:GS61R0.993
1:42457286:A:TD183V0.993
1:42457288:T:CF184L0.993
1:42457290:C:AF184L0.993
1:42457290:C:GF184L0.993
1:42457286:A:GD183G0.992
1:42456747:G:AS61N0.991
1:42457323:G:CK195N0.991
1:42457323:G:TK195N0.991
1:42459683:G:CK231N0.991
1:42459683:G:TK231N0.991
1:42457286:A:CD183A0.990
1:42457287:T:AD183E0.990
1:42457287:T:GD183E0.990
1:42456731:T:CF56L0.988
1:42456733:C:AF56L0.988
1:42456733:C:GF56L0.988
1:42459718:C:AA243D0.988
1:42456693:G:AG43D0.987
1:42457285:G:CD183H0.987

dbSNP variants (sampled 300 via entrez): RS1000014577 (1:42460994 G>A,T), RS1000283476 (1:42468105 A>C), RS1000397799 (1:42467837 T>C), RS1000445416 (1:42465585 G>A), RS1000546667 (1:42456445 T>C,G), RS1000602498 (1:42463253 G>A), RS1000785852 (1:42461527 G>A), RS1001073181 (1:42469630 G>A), RS1001687464 (1:42468179 G>A), RS1001727637 (1:42462326 A>T), RS1001781918 (1:42462640 G>C), RS1001849529 (1:42471635 C>G,T), RS1001959498 (1:42465292 C>T), RS1001993916 (1:42457501 C>T), RS1002066290 (1:42463426 G>A)

Disease associations

OMIM: gene MIM:609853 | disease phenotypes: MIM:618189

GenCC curated gene-disease

DiseaseClassificationInheritance
cardiomyopathy, dilated, 2cStrongAutosomal recessive
familial isolated dilated cardiomyopathySupportiveAutosomal dominant

Mondo (2): cardiomyopathy, dilated, 2c (MONDO:0032592), (MONDO:0015470)

Orphanet (0):

HPO phenotypes

23 total (23 of 23 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000407Sensorineural hearing impairment
HP:0000969Edema
HP:0001252Hypotonia
HP:0001522Death in infancy
HP:0001635Congestive heart failure
HP:0001644Dilated cardiomyopathy
HP:0001727Thromboembolic stroke
HP:0002092Pulmonary arterial hypertension
HP:0002151Increased circulating lactate concentration
HP:0002875Exertional dyspnea
HP:0003198Myopathy
HP:0003457EMG abnormality
HP:0003593Infantile onset
HP:0003623Neonatal onset
HP:0003819Death in childhood
HP:0011463Childhood onset
HP:0011675Arrhythmia
HP:0012378Fatigue
HP:0012664Reduced left ventricular ejection fraction
HP:0012764Orthopnea
HP:0025169Left ventricular systolic dysfunction
HP:0100578Lipoatrophy

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, decreases methylation3
Benzo(a)pyreneaffects methylation2
aristolochic acid Iincreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
beta-lapachoneincreases expression1
sodium arseniteaffects methylation1
cobaltous chloridedecreases expression1
benzo(e)pyreneincreases methylation1
di-n-butylphosphoric acidaffects expression1
jinfukangaffects cotreatment, increases expression1
Temozolomideincreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Cadmiumincreases expression1
Cisplatinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Methapyrileneincreases methylation1
Methyl Methanesulfonateincreases expression1
T-2 Toxinincreases expression1
Tobacco Smoke Pollutionaffects expression1
Urethanedecreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Vitamin K 3affects expression1
Particulate Matterdecreases expression, increases abundance1

Cellosaurus cell lines

2 cell lines: 2 induced pluripotent stem cell

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

CellosaurusNameCategorySex
CVCL_A0THMRIi028-AInduced pluripotent stem cellMale
CVCL_C0HSHMGUi003-AInduced pluripotent stem cellFemale

Clinical trials (associated diseases)

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