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

Gene ID: 29920, updated on 7-Apr-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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Location:
1q42.12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (225919878..225924250, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (225107658..225112030, complement)
105.20220307 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
  • 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. Pyrroline-5-carboxylate reductase 2 (PYCR2) deficiency causes hereditary spastic paraplaegia in late childhood. Sager G, et al. Eur J Paediatr Neurol, 2023 May. PMID 37141741
  2. Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Cancer Progression via Activating PI3K/AKT/mTOR Pathway. Yin F, et al. Dis Markers, 2021. PMID 34512817, Free PMC Article
  3. The upregulation of PYCR2 is associated with aggressive colon cancer progression and a poor prognosis. Wang S, et al. Biochem Biophys Res Commun, 2021 Oct 1. PMID 34332325
  4. 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
  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 (95) 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
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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 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_2023_10

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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