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    PYCR2 pyrroline-5-carboxylate reductase 2 [ Homo sapiens (human) ]

    Gene ID: 29920, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PYCR2provided by HGNC
    Official Full Name
    pyrroline-5-carboxylate reductase 2provided by HGNC
    Primary source
    HGNC:HGNC:30262
    See related
    Ensembl:ENSG00000143811 MIM:616406; AllianceGenome:HGNC:30262
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HLD10; P5CR2
    Summary
    This gene belongs to the pyrroline-5-carboxylate reductase family. The encoded mitochondrial protein catalyzes the conversion of pyrroline-5-carboxylate to proline, which is the last step in proline biosynthesis. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]
    Expression
    Ubiquitous expression in adrenal (RPKM 27.1), spleen (RPKM 24.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PYCR2 in Genome Data Viewer
    Location:
    1q42.12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (225919878..225924250, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (225107658..225112030, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (226107578..226111950, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene epoxide hydrolase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226033607-226034417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2630 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:226037931-226038477 Neighboring gene transmembrane protein 63A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2631 Neighboring gene MPRA-validated peak731 silencer Neighboring gene MPRA-validated peak732 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226067686-226068636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226074845-226075561 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226077715-226078432 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:226078433-226079150 and GRCh37_chr1:226079151-226079866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226083967-226084730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2635 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226087020-226087782 Neighboring gene left-right determination factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:226087783-226088545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226094136-226094909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226102994-226103938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226103939-226104881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226111847-226112496 Neighboring gene CRISPRi-validated cis-regulatory element chr1.11973 Neighboring gene microRNA 6741 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226126985-226127562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226131035-226131614 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226133351-226133930 Neighboring gene left-right determination factor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226138649-226139186 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:226146947-226147117 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Expanding the genotypic spectrum of PYCR2 and a common ancestry in Thai patients with hypomyelinating leukodystrophy 10. Manaspon C, et al. Am J Med Genet A, 2021 Oct. PMID 34037307
    2. PYCR2 promotes growth and aerobic glycolysis in human liver cancer by regulating the AKT signaling pathway. Wang S, et al. Biochem Biophys Res Commun, 2023 Nov 5. PMID 37708598
    3. Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Carcinogenesis by Modulating Microtubule-Associated Serine/Threonine Kinase-like/Wnt/β-Catenin Signaling. Lama Tamang R, et al. Cells, 2023 Jul 18. PMID 37508547, Free PMC Article
    4. PYCR2 Mutations cause a lethal syndrome of microcephaly and failure to thrive. Zaki MS, et al. Ann Neurol, 2016 Jul. PMID 27130255, Free PMC Article
    5. Disease variants of human Δ(1)-pyrroline-5-carboxylate reductase 2 (PYCR2). Patel SM, et al. Arch Biochem Biophys, 2021 May 30. PMID 33771508, Free PMC Article

    See all (110) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PYCR2 promotes growth and aerobic glycolysis in human liver cancer by regulating the AKT signaling pathway.
      Title: PYCR2 promotes growth and aerobic glycolysis in human liver cancer by regulating the AKT signaling pathway.
    2. Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Carcinogenesis by Modulating Microtubule-Associated Serine/Threonine Kinase-like/Wnt/beta-Catenin Signaling.
      Title: Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Carcinogenesis by Modulating Microtubule-Associated Serine/Threonine Kinase-like/Wnt/β-Catenin Signaling.
    3. LncRNA MALAT1 regulates growth of carcinoma of the lung through modulating miR-338-3p/PYCR2 axis.
      Title: LncRNA MALAT1 regulates growth of carcinoma of the lung through modulating miR-338-3p/PYCR2 axis.
    4. Pyrroline-5-carboxylate reductase 2 (PYCR2) deficiency causes hereditary spastic paraplaegia in late childhood.
      Title: Pyrroline-5-carboxylate reductase 2 (PYCR2) deficiency causes hereditary spastic paraplaegia in late childhood.
    5. Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Cancer Progression via Activating PI3K/AKT/mTOR Pathway.
      Title: Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Cancer Progression via Activating PI3K/AKT/mTOR Pathway.
    6. Expanding the genotypic spectrum of PYCR2 and a common ancestry in Thai patients with hypomyelinating leukodystrophy 10.
      Title: Expanding the genotypic spectrum of PYCR2 and a common ancestry in Thai patients with hypomyelinating leukodystrophy 10.
    7. The upregulation of PYCR2 is associated with aggressive colon cancer progression and a poor prognosis.
      Title: The upregulation of PYCR2 is associated with aggressive colon cancer progression and a poor prognosis.
    8. Disease variants of human Delta(1)-pyrroline-5-carboxylate reductase 2 (PYCR2).
      Title: Disease variants of human Δ(1)-pyrroline-5-carboxylate reductase 2 (PYCR2).
    9. Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
      Title: Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
    10. PYCR2-related syndrome represents a clinically recognizable condition in which PYCR2 mutations lead to protein dysfunction.
      Title: PYCR2 Mutations cause a lethal syndrome of microcephaly and failure to thrive.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Hypomyelinating leukodystrophy 10
    MedGen: C4225332 OMIM: 616420 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: LEFTY1

    Homology

    Clone Names

    • FLJ54750

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pyrroline-5-carboxylate reductase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in L-proline biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in L-proline biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to oxidative stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proline biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pyrroline-5-carboxylate reductase 2
    Names
    P5C reductase 2
    pyrroline-5-carboxylate reductase family member 2
    NP_001258610.1
    NP_037460.2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_044963.1 RefSeqGene

      Range
      5091..9463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271681.2 → NP_001258610.1  pyrroline-5-carboxylate reductase 2 isoform 2

      See identical proteins and their annotated locations for NP_001258610.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1.
      Source sequence(s)
      BC014868, BU538765, HY044355
      Consensus CDS
      CCDS73039.1
      UniProtKB/TrEMBL
      A0A087WTV6
      Related
      ENSP00000478165.1, ENST00000612039.4
      Conserved Domains (1) summary
      cl25964
      Location:1 → 194
      P5CR_dimer; Pyrroline-5-carboxylate reductase dimerisation

    2. NM_013328.4 → NP_037460.2  pyrroline-5-carboxylate reductase 2 isoform 1

      See identical proteins and their annotated locations for NP_037460.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AW166558, BC020553
      Consensus CDS
      CCDS31043.1
      UniProtKB/Swiss-Prot
      A8K798, Q7Z515, Q96C36, Q9Y5J4
      UniProtKB/TrEMBL
      A0A0S2Z5U6
      Related
      ENSP00000342502.6, ENST00000343818.11
      Conserved Domains (1) summary
      PLN02688
      Location:1 → 268
      PLN02688; pyrroline-5-carboxylate reductase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      225919878..225924250 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      225107658..225112030 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96C36.1 GenPept UniProtKB/Swiss-Prot:Q96C36

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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