PYCR1

gene
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Also known as P5C

Summary

PYCR1 (pyrroline-5-carboxylate reductase 1, HGNC:9721) is a protein-coding gene on chromosome 17q25.3, encoding Pyrroline-5-carboxylate reductase 1, mitochondrial (P32322). Oxidoreductase that catalyzes the last step in proline biosynthesis, which corresponds to the reduction of pyrroline-5-carboxylate to L-proline using NAD(P)H.

This gene encodes an enzyme that catalyzes the NAD(P)H-dependent conversion of pyrroline-5-carboxylate to proline. This enzyme may also play a physiologic role in the generation of NADP(+) in some cell types. The protein forms a homopolymer and localizes to the mitochondrion. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 5831 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autosomal recessive cutis laxa type 2B (Definitive, ClinGen) — +2 more curated relationships
  • Clinical variants (ClinVar): 376 total — 20 pathogenic, 16 likely-pathogenic
  • Phenotypes (HPO): 93
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_006907

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9721
Approved symbolPYCR1
Namepyrroline-5-carboxylate reductase 1
Location17q25.3
Locus typegene with protein product
StatusApproved
AliasesP5C
Ensembl geneENSG00000183010
Ensembl biotypeprotein_coding
OMIM179035
Entrez5831

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 18 protein_coding

ENST00000329875, ENST00000337943, ENST00000402252, ENST00000403172, ENST00000405481, ENST00000577624, ENST00000577756, ENST00000579366, ENST00000579698, ENST00000581271, ENST00000582198, ENST00000583564, ENST00000584848, ENST00000585215, ENST00000585244, ENST00000619204, ENST00000629768, ENST00000922965

RefSeq mRNA: 6 — MANE Select: NM_006907 NM_001282279, NM_001282280, NM_001282281, NM_001330523, NM_006907, NM_153824

CCDS: CCDS11794, CCDS11795, CCDS62365, CCDS62366, CCDS82221

Canonical transcript exons

ENST00000329875 — 7 exons

ExonStartEnd
ENSE000012950818193492681935147
ENSE000023706778193533781935516
ENSE000023850828193432681934489
ENSE000024274938193465381934745
ENSE000027265118193674881937300
ENSE000036796268193612381936193
ENSE000038905608193239181933376

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 96.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.5591 / max 139.1647, expressed in 1570 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
16886610.85061539
1688656.23321354
1688640.9921639
1688670.4832269

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225596.56gold quality
body of pancreasUBERON:000115095.84gold quality
parotid glandUBERON:000183192.22gold quality
ventricular zoneUBERON:000305391.39gold quality
pancreasUBERON:000126490.82gold quality
mucosa of transverse colonUBERON:000499190.69gold quality
saliva-secreting glandUBERON:000104489.49gold quality
pancreatic ductal cellCL:000207989.34silver quality
embryoUBERON:000092288.92gold quality
ganglionic eminenceUBERON:000402388.66gold quality
tibiaUBERON:000097988.34gold quality
minor salivary glandUBERON:000183088.33gold quality
body of stomachUBERON:000116188.05gold quality
cartilage tissueUBERON:000241887.84gold quality
stomachUBERON:000094586.96gold quality
periodontal ligamentUBERON:000826686.70gold quality
cortical plateUBERON:000534386.40gold quality
hindlimb stylopod muscleUBERON:000425286.16gold quality
mouth mucosaUBERON:000372986.12gold quality
olfactory bulbUBERON:000226486.08silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.92gold quality
type B pancreatic cellCL:000016984.20gold quality
islet of LangerhansUBERON:000000684.13gold quality
pituitary glandUBERON:000000783.79gold quality
diaphragmUBERON:000110383.74gold quality
lower esophagus mucosaUBERON:003583483.66gold quality
adenohypophysisUBERON:000219683.44gold quality
smooth muscle tissueUBERON:000113583.09gold quality
esophagus mucosaUBERON:000246982.69gold quality
olfactory segment of nasal mucosaUBERON:000538682.61gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-13yes27.92
E-CURD-112yes14.97
E-ANND-3yes11.31
E-MTAB-8271yes8.34
E-MTAB-9689no280.95
E-MTAB-10290no135.67

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR, TP53

miRNA regulators (miRDB)

24 targeting PYCR1, 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-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-449299.8768.253611
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-378A-5P99.6566.331311
HSA-MIR-715099.6266.801322
HSA-MIR-444199.4966.563216
HSA-MIR-608199.4866.071446
HSA-MIR-125399.1267.081688
HSA-MIR-450499.1069.141328
HSA-MIR-427099.0266.261987
HSA-MIR-5000-3P98.7965.631251
HSA-MIR-7113-3P98.7565.711120
HSA-MIR-323A-5P98.5965.13651
HSA-MIR-429098.5165.17907
HSA-MIR-4436A98.0564.831140
HSA-MIR-428797.5567.241247

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Mutagenesis and kinetic studies reveal the pivotal roles of the dinucleotide-binding Rossmann motif and residue Glu221 in the human enzyme Pyrroline-5-carboxylate reductase(P5CR). (PMID:16730026)
  • In Autosomal-recessive cutis laxa type 2, a single nucleotide change leads to a missense mutation adjacent to a splice junction in the gene encoding PYCR1. (PMID:19576563)
  • Mutations in PYCR1 cause cutis laxa with progeroid features. (PMID:19648921)
  • The phenotype caused by PYCR1 mutations corresponds to geroderma osteodysplasticum rather than ARCL2B. (PMID:21204221)
  • Mutation analysis revealed the presence of disease-causing variants in PYCR1, including a novel deletion of the entire PYCR1 gene in one family, and in each of the other patients the homozygous missense mutations. (PMID:21487760)
  • A novel mutation in PYCR1 causes an autosomal recessive cutis laxa with premature aging features in a family. (PMID:21567914)
  • The findings presented here suggest a mutation screening of PYCR1 and cardiovascular survey in patients with De Barsy syndrome (DBS). (PMID:22052856)
  • Identification of two new mutations in the PYCR1 gene in patients with autosomal recessive cutis laxa, type 2. (PMID:23531708)
  • Data suggest that DJ-1 and PYCR1 are on the same pathway of anti-oxidative stress protection of the cells. (PMID:23743200)
  • our current study presents the second largest group of patients with PYCR1-related ARCL and expands the clinical and genetic spectrum. (PMID:24035636)
  • confirming that indeed PYCR1 generates L-pipecolic acid from Delta(1)-piperideine-6-carboxylate (PMID:24431009)
  • Silencing of both PYCR1 and PYCR2 completely abolished anti-oxidation activity of RRM2B, demonstrating a functional collaboration of these metabolic enzymes in response to oxidative stress. (PMID:26733354)
  • Results indicate that single-nucleotide polymorphism (SNP)-derived mutations, R119G and G206W, enhance the rigidity of pyrroline-5-carboxylate reductase (P5CR) structure. (PMID:27677826)
  • Authors found that PYCR1 was highly expressed in prostate cancer tissues and then knocked down PYCR1 in PCa cell lines (DU145, PC-3 and LNCap) via lentivirus-mediated gene delivery and analyzed its biological function. (PMID:28078560)
  • experimental results indicate the R119G mutation could be an involving pathomechanism for Autosomal recessive cutis laxa . (PMID:28194412)
  • PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically (PMID:28258219)
  • these findings revealed that the mRNA and protein PYCR1 levels were significantly related to the poor outcome in either ER-negative or ER-positive breast cancer. PYCR1 could serve as a prognostic biomarker, therapeutic target and predictive biomarker for breast cancers. (PMID:28379297)
  • Authors describe a biosynthetic pathway exhibited by cells expressing mutant IDH1. By virtue of a change in cellular redox homeostasis, IDH1-mutated cells synthesize excess glutamine-derived proline through enhanced activity of pyrroline 5-carboxylate reductase 1 (PYCR1), coupled to NADH oxidation. (PMID:29562167)
  • we firmly establish biallelic mutations in POLR3A as the genetic cause of a recognizable, neonatal, Wiedemann-Rautenstrauch-like progeroid syndrome. Thus, we suggest that POLR3A mutations are causal for a portion of under-diagnosed early-onset segmental progeroid syndromes (PMID:30450527)
  • PYCR1 is negatively regulated by miR-488 and then promotes the occurrence and development of non-small-cell lung cancer and activates p38 MAPK pathway. (PMID:30605882)
  • High PYCR1 expression is associated with migration and Invasion of Nonsmall Cell Lung Cancer. (PMID:30916574)
  • acetylation of PYCR1 at K228 inhibits cell proliferation, while deacetylation of PYCR1 mediated by SIRT3 increases PYCR1’s activity. Our findings on the regulation of PYCR1 linked proline metabolism with SIRT3, CBP and cell growth, thus providing a potential approach for cancer therapy. (PMID:31108370)
  • PYCR1 plays a role in the proliferation, epithelial-mesenchymal transition and drug resistance by regulating STAT3-mediated p38 MAPK and NF-kappaB signalling pathways in the colorectal cancer cells.PYCR1 is highly espressed in tissues and cells of the colorectal cancer patients. (PMID:31606203)
  • PYCR1 interference inhibits cell growth and survival via c-Jun N-terminal kinase/insulin receptor substrate 1 (JNK/IRS1) pathway in hepatocellular cancer. (PMID:31619254)
  • Mitochondrial oxidative stress by Lon-PYCR1 maintains an immunosuppressive tumor microenvironment that promotes cancer progression and metastasis. (PMID:31987921)
  • High PYCR1 expression is associated with lung adenocarcinoma. (PMID:32133692)
  • Oncogenic Kaposi’s sarcoma-associated herpesvirus (KSHV) K1 oncoprotein interacted with and activated PYCR enzyme, increasing intracellular proline concentration. Consequently, the K1-PYCR interaction promoted tumor cell growth in 3D spheroid culture and tumorigenesis in nude mice. This study demonstrates that an increase of proline biosynthesis induced by K1-PYCR interaction is critical for KSHV-mediated tumorigenesis. (PMID:32213586)
  • Dysregulation of USP18/FTO/PYCR1 signaling network promotes bladder cancer development and progression. (PMID:33461172)
  • PYCR1 promotes bladder cancer by affecting the Akt/Wnt/beta-catenin signaling. (PMID:33689096)
  • MiR-328-3p inhibits lung adenocarcinoma-genesis by downregulation PYCR1. (PMID:33706104)
  • Deciphering the effects of PYCR1 on cell function and its associated mechanism in hepatocellular carcinoma. (PMID:34239351)
  • MiR-1207-5p targets PYCR1 to inhibit the progression of prostate cancer. (PMID:34461437)
  • MicroRNA hsa-miR-150-5p inhibits nasopharyngeal carcinogenesis by suppressing PYCR1 (pyrroline-5-carboxylate reductase 1). (PMID:34696668)
  • Proline synthesis through PYCR1 is required to support cancer cell proliferation and survival in oxygen-limiting conditions. (PMID:35108535)
  • Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix. (PMID:35760868)
  • The role of PYCR1 in inhibiting 5-fluorouracil-induced ferroptosis and apoptosis through SLC25A10 in colorectal cancer. (PMID:36104652)
  • SENP3 affects the expression of PYCR1 to promote bladder cancer proliferation and EMT transformation by deSUMOylation of STAT3. (PMID:36227136)
  • LINC01123 acts as an oncogenic driver in lung adenocarcinoma by regulating the miR-4766-5p/PYCR1 axis. (PMID:36994814)
  • Effects of PYCR1 on prognosis and immunotherapy plus tyrosine kinase inhibition responsiveness in metastatic renal cell carcinoma patients. (PMID:37517099)
  • IGF1R-phosphorylated PYCR1 facilitates ELK4 transcriptional activity and sustains tumor growth under hypoxia. (PMID:37777542)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriopycr1bENSDARG00000098639
danio_reriopycr1aENSDARG00000102254
mus_musculusPycr1ENSMUSG00000025140
rattus_norvegicusPycr1ENSRNOG00000036682
drosophila_melanogasterP5cr-2FBGN0038516
caenorhabditis_elegansWBGENE00010924

Paralogs (3): PYCR3 (ENSG00000104524), PYCR2 (ENSG00000143811), NOXRED1 (ENSG00000165555)

Protein

Protein identifiers

Pyrroline-5-carboxylate reductase 1, mitochondrialP32322 (reviewed: P32322)

All UniProt accessions (13): E2QRB3, P32322, J3KQ22, J3KSA9, J3KTA8, J3QKT3, J3QKT4, J3QL23, J3QL24, J3QL32, J3QLK9, J3QR88, J3QRZ0

UniProt curated annotations — full annotation on UniProt →

Function. Oxidoreductase that catalyzes the last step in proline biosynthesis, which corresponds to the reduction of pyrroline-5-carboxylate to L-proline using NAD(P)H. At physiologic concentrations, has higher specific activity in the presence of NADH. Involved in the cellular response to oxidative stress.

Subunit / interactions. Homodecamer; composed of 5 homodimers (PubMed:16730026, PubMed:28258219, Ref.19). Interacts with LTO1.

Subcellular location. Mitochondrion.

Disease relevance. Cutis laxa, autosomal recessive, 2B (ARCL2B) [MIM:612940] A disorder characterized by an excessive congenital skin wrinkling, a large fontanelle with delayed closure, a typical facial appearance with downslanting palpebral fissures, a general connective tissue weakness, and varying degrees of growth and developmental delay and neurological abnormalities. Patients do not manifest metabolic abnormalities. The disease is caused by variants affecting the gene represented in this entry. Cutis laxa, autosomal recessive, 3B (ARCL3B) [MIM:614438] A disorder characterized by an aged appearance with distinctive facial features, sparse hair, ophthalmologic abnormalities, intrauterine growth retardation, and cutis laxa. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Subject to competitive inhibition by the reaction product proline. Subject to competitive inhibition by stearoyl coenzyme A.

Pathway. Amino-acid biosynthesis; L-proline biosynthesis; L-proline from L-glutamate 5-semialdehyde: step 1/1.

Similarity. Belongs to the pyrroline-5-carboxylate reductase family.

Isoforms (3)

UniProt IDNamesCanonical?
P32322-11yes
P32322-22
P32322-33

RefSeq proteins (6): NP_001269208, NP_001269209, NP_001269210, NP_001317452, NP_008838, NP_722546 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000304Pyrroline-COOH_reductaseFamily
IPR0089276-PGluconate_DH-like_C_sfHomologous_superfamily
IPR028939P5C_Rdtase_cat_NDomain
IPR029036P5CR_dimerDomain
IPR036291NAD(P)-bd_dom_sfHomologous_superfamily
IPR053790P5CR-like_CSConserved_site

Pfam: PF03807, PF14748

Enzyme classification (BRENDA):

  • EC 1.5.1.2 — pyrroline-5-carboxylate reductase (BRENDA: 43 organisms, 56 substrates, 140 inhibitors, 118 Km, 52 kcat entries)

Substrate kinetics (BRENDA)

11 substrates with measured Km, best-characterized 11. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
1-PYRROLINE-5-CARBOXYLATE0.02–2.88741
NADH0.025–1.5526
NADPH0.006–0.71924
DL-PYRROLINE-5-CARBOXYLATE0.051–0.625
L-PROLINE0.12–505
NADP+0.093–3.065
NAD+0.151–10.53
L-PYRROLINE-5-CARBOXYLATE0.332
3,4-DEHYDRO-L-PROLINE0.1411
DELTA1-PYRROLINE-3-HYDROXY-5-CARBOXYLATE4.41
PYRROLINE-5-CARBOXYLATE0

Catalyzed reactions (Rhea), 2 shown:

  • L-proline + NAD(+) = (S)-1-pyrroline-5-carboxylate + NADH + 2 H(+) (RHEA:14105)
  • L-proline + NADP(+) = (S)-1-pyrroline-5-carboxylate + NADPH + 2 H(+) (RHEA:14109)

UniProt features (69 total): binding site 18, helix 17, sequence variant 11, strand 10, modified residue 3, splice variant 2, mutagenesis site 2, sequence conflict 2, initiator methionine 1, chain 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

47 structures, top 30 by resolution.

PDBMethodResolution (Å)
9P0RX-RAY DIFFRACTION1.49
9S04X-RAY DIFFRACTION1.57
9P0SX-RAY DIFFRACTION1.58
8TD7X-RAY DIFFRACTION1.61
8TD2X-RAY DIFFRACTION1.65
9S01X-RAY DIFFRACTION1.65
9S02X-RAY DIFFRACTION1.65
9P0UX-RAY DIFFRACTION1.66
8TD3X-RAY DIFFRACTION1.67
9RZZX-RAY DIFFRACTION1.7
8TD8X-RAY DIFFRACTION1.71
8TCXX-RAY DIFFRACTION1.72
8TCVX-RAY DIFFRACTION1.74
9P0QX-RAY DIFFRACTION1.74
6XP1X-RAY DIFFRACTION1.75
8TD9X-RAY DIFFRACTION1.75
9Q46X-RAY DIFFRACTION1.75
8TD4X-RAY DIFFRACTION1.76
9P0TX-RAY DIFFRACTION1.79
9Q45X-RAY DIFFRACTION1.79
8TDCX-RAY DIFFRACTION1.8
9P0VX-RAY DIFFRACTION1.8
8TD5X-RAY DIFFRACTION1.81
8VREX-RAY DIFFRACTION1.83
5UAVX-RAY DIFFRACTION1.85
5UAWX-RAY DIFFRACTION1.85
5UAXX-RAY DIFFRACTION1.85
8DKGX-RAY DIFFRACTION1.85
8TD1X-RAY DIFFRACTION1.88
5UAUX-RAY DIFFRACTION1.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P32322-F189.980.84

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 (18): 56; 56; 69–72; 70; 71; 95–97; 97; 164; 230; 237; 238; 6–11

Post-translational modifications (3): 2, 278, 301

Mutagenesis-validated functional residues (2):

PositionPhenotype
221reduced enzyme activity.
238decreased pyrroline-5-carboxylate reductase activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8964539Glutamate and glutamine metabolism

MSigDB gene sets: 371 (showing top): MODULE_93, GOBP_NEGATIVE_REGULATION_OF_NEURON_APOPTOTIC_PROCESS, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_GLUTAMINE_FAMILY_AMINO_ACID_BIOSYNTHETIC_PROCESS, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, GOBP_AMINO_ACID_BIOSYNTHETIC_PROCESS, GOBP_GLUTAMINE_FAMILY_AMINO_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, SCHUHMACHER_MYC_TARGETS_UP, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY

GO Biological Process (6): cellular response to oxidative stress (GO:0034599), regulation of mitochondrial membrane potential (GO:0051881), L-proline biosynthetic process (GO:0055129), negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377), obsolete proline biosynthetic process (GO:0006561), amino acid biosynthetic process (GO:0008652)

GO Molecular Function (4): pyrroline-5-carboxylate reductase activity (GO:0004735), identical protein binding (GO:0042802), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of amino acids and derivatives1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
response to oxidative stress1
cellular response to chemical stress1
regulation of membrane potential1
L-proline metabolic process1
glutamate family amino acid biosynthetic process1
neuron intrinsic apoptotic signaling pathway in response to oxidative stress1
negative regulation of neuron apoptotic process1
negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway1
regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway1
amino acid metabolic process1
biosynthetic process1
oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor1
protein binding1
binding1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1

Protein interactions and networks

STRING

1820 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PYCR1ALDH18A1P54886956
PYCR1JAG2Q9Y219949
PYCR1PCF11O94913918
PYCR1GORABQ5T7V8823
PYCR1ATP6V0A2Q9Y487808
PYCR1EFEMP2O95967779
PYCR1ALDH4A1P30038768
PYCR1PRODHO43272762
PYCR1LTO1Q8WV07757
PYCR1POLR2AP24928753
PYCR1PRODHO43272734
PYCR1OATP04181712
PYCR1FBLN5Q9UBX5693
PYCR1TRIM11Q96F44667
PYCR1PLEKHF1Q96S99666

IntAct

146 interactions, top by confidence:

ABTypeScore
CDC23BUB1Bpsi-mi:“MI:0914”(association)0.790
ANAPC16BUB1Bpsi-mi:“MI:0914”(association)0.730
ANAPC2BUB1Bpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
PYCR1PYCR1psi-mi:“MI:0407”(direct interaction)0.680
PYCR1PYCR1psi-mi:“MI:0915”(physical association)0.680
repPOLA1psi-mi:“MI:0914”(association)0.670
PARK7PYCR1psi-mi:“MI:0915”(physical association)0.610
PYCR1PARK7psi-mi:“MI:0403”(colocalization)0.610
PYCR1PARK7psi-mi:“MI:0915”(physical association)0.610
TNPO2PYCR1psi-mi:“MI:0915”(physical association)0.560
HNRNPH2PLOD2psi-mi:“MI:0914”(association)0.530
PYCR1PYCR3psi-mi:“MI:0914”(association)0.530
repPYCR1psi-mi:“MI:0914”(association)0.460
AIFM1HAX1psi-mi:“MI:2364”(proximity)0.420
AIFM1SEC16Apsi-mi:“MI:2364”(proximity)0.420
HTRA2HAX1psi-mi:“MI:2364”(proximity)0.420

BioGRID (273): PYCR1 (Affinity Capture-MS), PYCR1 (Affinity Capture-MS), PYCR1 (Affinity Capture-MS), PYCR1 (Affinity Capture-MS), NUDT5 (Affinity Capture-MS), PYCR2 (Affinity Capture-MS), KLHDC10 (Affinity Capture-MS), PYCRL (Affinity Capture-MS), CCDC47 (Co-fractionation), PYCR1 (Co-fractionation), PYCR1 (Affinity Capture-MS), PYCR1 (Affinity Capture-MS), PYCR1 (Affinity Capture-MS), PYCR1 (Proximity Label-MS), PYCR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0C1E1C6, A0A348AXY1, A0A411KUQ8, A1CP85, B6HAA7, B8M0U4, C5PA86, L0E163, P00927, P0CM22, P0CM23, P32263, P32322, P40386, P41835, P54889, Q00055, Q09921, Q17QJ7, Q20848, Q39659, Q4P219, Q4PNS1, Q4R6W7, Q4WEE0, Q55E34, Q58DT4, Q59W33, Q5R9X6, Q5RAQ3, Q5SPD7, Q5ZKA5, Q6AY23, Q6CR99, Q6FN96, Q6J5J3, Q6ZZF4, Q759G5, Q7ZA43, Q8K009

Diamond homologs: A0A411KUQ8, P32322, Q12641, Q12740, Q17QJ7, Q4R6W7, Q58D08, Q58DT4, Q5R9X6, Q6AY23, Q922Q4, Q922W5, A0A348AXY1, A1L2Q8, E0TY11, O04016, P0A9L8, P0A9L9, P0C1E4, P0C1E5, P0CI77, P17817, P22008, P27771, P32263, P46725, P52053, P54552, P54893, P54904, P74572, P9WHU6, P9WHU7, Q04708, Q20848, Q4R531, Q53H96, Q5PQJ6, Q5RAQ3, Q5SPD7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 153 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
Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components742.3×8e-08
Inactivation of APC/C via direct inhibition of the APC/C complex734.6×1e-07
Phosphorylation of the APC/C631.1×2e-06
Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase629.7×2e-06
Aberrant regulation of mitotic exit in cancer due to RB1 defects629.7×2e-06
APC-Cdc20 mediated degradation of Nek2A728.2×3e-07
APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint728.2×3e-07
Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins727.2×4e-07

GO biological processes:

GO termPartnersFoldFDR
protein branched polyubiquitination638.9×3e-06
anaphase-promoting complex-dependent catabolic process737.8×4e-07
regulation of meiotic cell cycle635.4×4e-06
protein K11-linked ubiquitination618.1×2e-04
regulation of mitotic cell cycle611.1×2e-03
protein K48-linked ubiquitination79.1×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic20
Likely pathogenic16
Uncertain significance133
Likely benign150
Benign16

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
13190NM_006907.4(PYCR1):c.797G>A (p.Arg266Gln)Pathogenic
13191NM_006907.4(PYCR1):c.616G>T (p.Gly206Trp)Pathogenic
13192NM_006907.4(PYCR1):c.618_633+7delPathogenic
13195NM_006907.4(PYCR1):c.11del (p.Gly4fs)Pathogenic
13196NM_006907.4(PYCR1):c.355C>G (p.Arg119Gly)Pathogenic
2082773NM_006907.4(PYCR1):c.570_571insA (p.Gly191fs)Pathogenic
2840833NM_006907.4(PYCR1):c.486_517del (p.Glu163fs)Pathogenic
29864NM_006907.4(PYCR1):c.345del (p.Arg116fs)Pathogenic
3069061NM_006907.4(PYCR1):c.148del (p.Gly49_Val50insTer)Pathogenic
3662010NM_006907.4(PYCR1):c.138+2T>GPathogenic
3711852NM_006907.4(PYCR1):c.633+2T>GPathogenic
4720032NM_006907.4(PYCR1):c.118del (p.Ala40fs)Pathogenic
4724740NM_006907.4(PYCR1):c.509_513del (p.Val170fs)Pathogenic
4725770NM_006907.4(PYCR1):c.176_194del (p.Thr59fs)Pathogenic
4764024NM_006907.4(PYCR1):c.663_670dup (p.Pro224fs)Pathogenic
488457NM_006907.4(PYCR1):c.59dup (p.Ala21fs)Pathogenic
694681NM_006907.4(PYCR1):c.11G>T (p.Gly4Val)Pathogenic
694712NM_006907.4(PYCR1):c.540+1G>APathogenic
871527NM_006907.4(PYCR1):c.349G>T (p.Val117Phe)Pathogenic
996064NM_006907.4(PYCR1):c.67+2T>APathogenic
1526132NM_006907.4(PYCR1):c.540+1G>TLikely pathogenic
1526245NM_006907.4(PYCR1):c.556G>T (p.Asp186Tyr)Likely pathogenic
2572601NM_006907.4(PYCR1):c.386_387insCGCA (p.Glu130fs)Likely pathogenic
2882123NM_006907.4(PYCR1):c.291_294dup (p.Val99fs)Likely pathogenic
3583145NM_006907.4(PYCR1):c.394_400del (p.Ala132fs)Likely pathogenic
3583146NM_006907.4(PYCR1):c.318+1G>ALikely pathogenic
3583147NM_006907.4(PYCR1):c.231dup (p.Ile78fs)Likely pathogenic
392367NM_006907.4(PYCR1):c.798-1G>ALikely pathogenic
4076962NM_006907.4(PYCR1):c.181C>T (p.Gln61Ter)Likely pathogenic
426550NM_006907.4(PYCR1):c.637G>A (p.Ala213Thr)Likely pathogenic

SpliceAI

1055 predictions. Top by Δscore:

VariantEffectΔscore
17:81933372:GCTCC:Gacceptor_gain1.0000
17:81933373:CTCC:Cacceptor_gain1.0000
17:81933373:CTCCC:Cacceptor_gain1.0000
17:81933374:TCC:Tacceptor_gain1.0000
17:81933374:TCCCT:Tacceptor_gain1.0000
17:81933375:CC:Cacceptor_gain1.0000
17:81933375:CCC:Cacceptor_gain1.0000
17:81933376:CC:Cacceptor_gain1.0000
17:81933377:C:CCacceptor_gain1.0000
17:81934386:T:Adonor_gain1.0000
17:81934486:CCCC:Cacceptor_gain1.0000
17:81934487:CCC:Cacceptor_gain1.0000
17:81934487:CCCC:Cacceptor_gain1.0000
17:81934488:CC:Cacceptor_gain1.0000
17:81934488:CCC:Cacceptor_gain1.0000
17:81934489:CC:Cacceptor_gain1.0000
17:81934490:C:Aacceptor_loss1.0000
17:81934491:T:Cacceptor_loss1.0000
17:81934647:A:ACdonor_gain1.0000
17:81934648:C:CCdonor_gain1.0000
17:81934924:A:ACdonor_gain1.0000
17:81934925:C:CAdonor_gain1.0000
17:81934978:TCC:Tdonor_gain1.0000
17:81934984:T:TAdonor_gain1.0000
17:81935143:AGCTT:Aacceptor_gain1.0000
17:81935145:CTT:Cacceptor_gain1.0000
17:81935145:CTTC:Cacceptor_loss1.0000
17:81935146:TT:Tacceptor_gain1.0000
17:81935147:TC:Tacceptor_loss1.0000
17:81935148:C:CCacceptor_gain1.0000

AlphaMissense

2066 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:81935097:G:CN123K0.999
17:81935097:G:TN123K0.999
17:81934354:C:GA257P0.998
17:81934711:C:TG192D0.998
17:81934332:C:GR264P0.997
17:81934715:C:AG191W0.997
17:81934944:A:CS174R0.997
17:81934944:A:TS174R0.997
17:81934946:T:GS174R0.997
17:81934951:C:TG172E0.997
17:81934952:C:AG172W0.997
17:81935075:C:AG131W0.997
17:81935362:C:TG98D0.997
17:81933371:A:GL268P0.996
17:81934723:A:GL188P0.996
17:81934727:C:GA187P0.996
17:81934936:C:TG177D0.996
17:81934942:C:TG175D0.996
17:81935060:C:GA136P0.996
17:81935075:C:GG131R0.996
17:81935075:C:TG131R0.996
17:81935108:A:GC120R0.996
17:81935365:G:TA97D0.996
17:81936162:G:CS33R0.996
17:81936162:G:TS33R0.996
17:81936164:T:GS33R0.996
17:81934353:G:TA257D0.995
17:81934439:C:AK228N0.995
17:81934439:C:GK228N0.995
17:81934482:G:TA214D0.995

dbSNP variants (sampled 300 via entrez): RS1000620594 (17:81938144 A>T), RS1000962824 (17:81933173 GAA>G), RS1001510551 (17:81934791 C>T), RS1002232798 (17:81931890 C>T), RS1002289761 (17:81937135 A>AG), RS1002941338 (17:81937433 C>A,G,T), RS1002965607 (17:81934747 T>A,C), RS1003065407 (17:81932668 G>A,C), RS1003276150 (17:81936199 G>A), RS1003548171 (17:81932326 T>C,G), RS1004602308 (17:81934394 A>G), RS1005408145 (17:81933941 G>A,C), RS1005428765 (17:81938902 C>T), RS1005693203 (17:81936468 G>A), RS1005701798 (17:81936768 G>A,C,T)

Disease associations

OMIM: gene MIM:179035 | disease phenotypes: MIM:612940, MIM:614438

GenCC curated gene-disease

DiseaseClassificationInheritance
PYCR1-related de Barsy syndromeDefinitiveAutosomal recessive
autosomal recessive cutis laxa type 2BDefinitiveAutosomal recessive
geroderma osteodysplasticaSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
autosomal recessive cutis laxa type 2BDefinitiveAR

Mondo (5): autosomal recessive cutis laxa type 2B (MONDO:0013051), PYCR1-related de Barsy syndrome (MONDO:0013755), cutis laxa (MONDO:0016175), microcephaly (MONDO:0001149), geroderma osteodysplastica (MONDO:0009271)

Orphanet (4): Autosomal recessive cutis laxa type 2B (Orphanet:357064), Cutis laxa (Orphanet:209), PYCR1-related De Barsy syndrome (Orphanet:293633), De Barsy syndrome (Orphanet:2962)

HPO phenotypes

93 total (30 of 93 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000218High palate
HP:0000233Thin vermilion border
HP:0000238Hydrocephalus
HP:0000239Large fontanelles
HP:0000252Microcephaly
HP:0000272Malar flattening
HP:0000303Mandibular prognathia
HP:0000316Hypertelorism
HP:0000325Triangular face
HP:0000337Broad forehead
HP:0000343Long philtrum
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000411Protruding ear
HP:0000414Bulbous nose
HP:0000418Narrow nasal ridge
HP:0000430Underdeveloped nasal alae
HP:0000460Narrow nose
HP:0000478Abnormality of the eye
HP:0000482Microcornea
HP:0000490Deeply set eye
HP:0000494Downslanted palpebral fissures
HP:0000501Glaucoma
HP:0000504Abnormality of vision
HP:0000518Cataract
HP:0000592Blue sclerae
HP:0000601Hypotelorism

GWAS associations

0 associations (top):

MeSH disease descriptors (4)

DescriptorNameTree numbers
D003483Cutis LaxaC16.320.850.180; C17.300.230; C17.800.827.180
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
C567855Cutis Laxa, Autosomal Recessive, Type IIB (supp.)
C537799Gerodermia osteodysplastica (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4296002 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 11,884 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL673PARGYLINE411,884

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

ChEMBL bioactivities

5 potent at pChembl≥5 of 41 total, top 5 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.30Kd50.33nMCHEMBL5653589
7.30ED5050.33nMCHEMBL5653589
5.06IC508800nMCHEMBL4442920
5.04IC509200nMCHEMBL4452615
5.01IC509700nMCHEMBL4462797

PubChem BioAssay actives

4 with measured affinity, of 73 total; 4 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]benzamide2149158: Binding affinity to human PYCR1 incubated for 45 mins by Kinobead based pull down assaykd0.0503uM
N-[(4-bromophenyl)methyl]-N-methylprop-2-yn-1-amine1589018: Inhibition of 6x-His-tagged and SUMO tagged human PYCR1 expressed in Escherichia coli BL21 (DE3) cells assessed as reduction in NADH oxidation incubated for 1 hric508.8000uM
N-[(2,4-dichlorophenyl)methyl]-N-methylprop-2-yn-1-amine1589018: Inhibition of 6x-His-tagged and SUMO tagged human PYCR1 expressed in Escherichia coli BL21 (DE3) cells assessed as reduction in NADH oxidation incubated for 1 hric509.2000uM
N-[(4-iodophenyl)methyl]-N-methylprop-2-yn-1-amine1589018: Inhibition of 6x-His-tagged and SUMO tagged human PYCR1 expressed in Escherichia coli BL21 (DE3) cells assessed as reduction in NADH oxidation incubated for 1 hric509.7000uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases methylation, affects cotreatment4
Cadmium Chloridedecreases expression, increases abundance, increases expression4
bisphenol Adecreases expression2
Acetaminophendecreases expression2
Cadmiumincreases abundance, increases expression2
Estradiolincreases expression2
Plant Extractsaffects cotreatment, decreases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
chloroacetaldehydeaffects expression1
benzo(b)fluoranthenedecreases expression, affects cotreatment1
nobiletindecreases expression, decreases reaction1
sodium arsenatedecreases expression, decreases reaction1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression1
benz(a)anthraceneaffects cotreatment, decreases expression1
chryseneaffects cotreatment, decreases expression1
perfluorooctane sulfonic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
LDN 193189affects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1

ChEMBL screening assays

12 unique, capped per target: 12 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4119009BindingBinding affinity to PYCR1 in human NCI-H358 cells at 1 uM by mass spectrometry based pull down assayStudies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. — Bioorg Med Chem

Cellosaurus cell lines

6 cell lines: 6 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D1QAAbcam K-562 PYCR1 KOCancer cell lineFemale
CVCL_D2LWAbcam Raji PYCR1 KOCancer cell lineMale
CVCL_TH84HAP1 PYCR1 (-) 1Cancer cell lineMale
CVCL_TH85HAP1 PYCR1 (-) 2Cancer cell lineMale
CVCL_TH86HAP1 PYCR1 (-) 3Cancer cell lineMale
CVCL_WQ44Abcam Jurkat PYCR1 KOCancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03887208PHASE1/PHASE2COMPLETEDTherapy of Scars and Cutis Laxa With Autologous Adipose Derived Mesenchymal Stem Cells
NCT01293864Not specifiedTERMINATEDStructural Analysis of Human Tissue
NCT01658163Not specifiedCOMPLETEDUse of 2-octyl-cyanoacrylate Together With a Self-adhering Mesh
NCT06330324Not specifiedENROLLING_BY_INVITATIONReproductive Options in Inherited Skin Diseases
NCT06330350Not specifiedRECRUITINGQualitative Study in Patients With Genodermatoses and Healthcare Professionals on Reproductive Counselling
NCT07614997Not specifiedNOT_YET_RECRUITINGEffectiveness and Safety of the Ulthera® System for Skin Laxity in the Lower Face, Submentum and Neck
NCT05518188PHASE1/PHASE2RECRUITINGMelpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT00001639Not specifiedCOMPLETEDEvaluation of Patients With Unresolved Chromosome Abnormalities
NCT01151462Not specifiedWITHDRAWNPostnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
NCT01565005Not specifiedCOMPLETEDMicrocephaly Genetic Deficiency in Neural Progenitors
NCT02510170Not specifiedCOMPLETEDFetal and Maternal Head Circumference During Pregnancy in Israeli Population
NCT02741882Not specifiedCOMPLETEDZika and Microcephaly: Case-control Study
NCT02943304Not specifiedCOMPLETEDNeurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero
NCT03255369Not specifiedUNKNOWNVertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF)
NCT03325946Not specifiedRECRUITINGThe FBRI VTC Neuromotor Research Clinic
NCT03330600Not specifiedCOMPLETEDEfficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome
NCT03548779Not specifiedCOMPLETEDNorth Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
NCT03651687Not specifiedCOMPLETEDGuangzhou Surveillance and Clinical Study in Microcephaly (GSCSM)
NCT03922594Not specifiedTERMINATEDSurveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia
NCT04816175Not specifiedCOMPLETEDIntensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay
NCT05322980Not specifiedCOMPLETEDSummary of Infants Weighing 500 Grams or Less
NCT06019182Not specifiedRECRUITINGMEHMO Natural History and Biomarkers
NCT06566066Not specifiedRECRUITINGRegister for Patients With Thyroid Hormone Resistance.