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    CRPPA CDP-L-ribitol pyrophosphorylase A [ Homo sapiens (human) ]

    Gene ID: 729920, updated on 5-Mar-2024

    Summary

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    Official Symbol
    CRPPAprovided by HGNC
    Official Full Name
    CDP-L-ribitol pyrophosphorylase Aprovided by HGNC
    Primary source
    HGNC:HGNC:37276
    See related
    Ensembl:ENSG00000214960 MIM:614631; AllianceGenome:HGNC:37276
    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
    Nip; ISPD; hISPD; MDDGA7; MDDGC7; LGMDR20
    Summary
    This gene encodes a 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein. Mutations in this gene are the cause of Walker-Warburg syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2012]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7p21.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (16087525..16421538, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (16220757..16551280, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (16127150..16461163, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927558 Neighboring gene uncharacterized LOC105375167 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:15821381-15822127 Neighboring gene Sharpr-MPRA regulatory region 14985 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:15980075-15980647 Neighboring gene Sharpr-MPRA regulatory region 6485 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:16116228-16117427 Neighboring gene NANOG hESC enhancer GRCh37_chr7:16117754-16118288 Neighboring gene MPRA-validated peak6410 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:16254865-16255366 Neighboring gene ribosomal protein L36a pseudogene 29 Neighboring gene CRPPA antisense RNA 1 Neighboring gene MPRA-validated peak6411 silencer Neighboring gene uncharacterized LOC105375168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:16541518-16542018 Neighboring gene NANOG hESC enhancer GRCh37_chr7:16551577-16552078 Neighboring gene sclerostin domain containing 1 Neighboring gene leucine rich repeat containing 72

    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. A splice site mutation c.1251G>A of ISPD gene is a common cause of congenital muscular dystrophy in Chinese patients. Song D, et al. Clin Genet, 2020 May. PMID 31909476
    2. Recent advancements in understanding mammalian O-mannosylation. Sheikh MO, et al. Glycobiology, 2017 Sep 1. PMID 28810660, Free PMC Article
    3. ISPD mutations account for a small proportion of Italian Limb Girdle Muscular Dystrophy cases. Magri F, et al. BMC Neurol, 2015 Sep 24. PMID 26404900, Free PMC Article
    4. ISPD gene homozygous deletion identified by SNP array confirms prenatal manifestation of Walker-Warburg syndrome. Trkova M, et al. Eur J Med Genet, 2015 Aug. PMID 26087224
    5. A novel homozygous ISPD gene mutation causing phenotype variability in a consanguineous family. Baranello G, et al. Neuromuscul Disord, 2015 Jan. PMID 25444434

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A splice site mutation c.1251G>A of ISPD gene is a common cause of congenital muscular dystrophy in Chinese patients.
      Title: A splice site mutation c.1251G>A of ISPD gene is a common cause of congenital muscular dystrophy in Chinese patients.
    2. Hsa_circ_0079480 promotes tumor progression in acute myeloid leukemia via miR-654-3p/HDGF axis.
      Title: Hsa_circ_0079480 promotes tumor progression in acute myeloid leukemia via miR-654-3p/HDGF axis.
    3. ISPD and FKTN are essential for the incorporation of ribitol into alpha-dystroglycan.
      Title: ISPD produces CDP-ribitol used by FKTN and FKRP to transfer ribitol phosphate onto α-dystroglycan.
    4. data suggest that the genetic heterogeneity of Limb Girdle Muscular Dystrophy with and without alpha-DG defects is greater than previously realized.
      Title: ISPD mutations account for a small proportion of Italian Limb Girdle Muscular Dystrophy cases.
    5. ISPD gene homozygous deletion as a prenatal manifestation of Walker-Warburg syndrome has been found in 3 female fetuses of one family.
      Title: ISPD gene homozygous deletion identified by SNP array confirms prenatal manifestation of Walker-Warburg syndrome.
    6. Reduced levels of GYLTL1B and ISPD mRNA associated with increased patient mortality and are the likely cause of alphaDG hypoglycosylation in ccRCC.
      Title: Downregulation of dystroglycan glycosyltransferases LARGE2 and ISPD associate with increased mortality in clear cell renal cell carcinoma.
    7. study describes a new homozygous missense mutation c.367G>A (p.Gly123Arg) in the ISPD gene in a family of Pakistani origin with 2 cousins from consanguineous parents affected with a congenital muscular dystrophy (CMD) /early limb-girdle muscular dystrophy intermediate phenotype and CMD respectively
      Title: A novel homozygous ISPD gene mutation causing phenotype variability in a consanguineous family.
    8. study report the involvement of the ISPD gene in milder dystroglycanopathy phenotypes ranging from congenital muscular dystrophy to limb-girdle muscular dystrophy and identified allelic ISPD variants in nine cases belonging to seven families
      Title: ISPD gene mutations are a common cause of congenital and limb-girdle muscular dystrophies.
    9. we identified a novel homozygous c.161G>C/p.G54A variant in ISPD in patients with limb-girdle muscular dystrophy
      Title: Limb-girdle muscular dystrophy with α-dystroglycan deficiency and mutations in the ISPD gene.
    10. TMEM5 mutations were frequently associated with gonadal dysgenesis and neural tube defects, and ISPD mutations were frequently associated with brain vascular anomalies.
      Title: Identification of mutations in TMEM5 and ISPD as a cause of severe cobblestone lissencephaly.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    EBI GWAS Catalog

    Description
    Impact of four loci on serum tamsulosin hydrochloride concentration.
    EBI GWAS Catalog

    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

    Homology

    Clone Names

    • FLJ42815

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D-ribitol-5-phosphate cytidylyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables D-ribitol-5-phosphate cytidylyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cytidylyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in isoprenoid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein O-linked mannosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein O-linked mannosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    D-ribitol-5-phosphate cytidylyltransferase
    Names
    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein
    4-diphosphocytidyl-2C-methyl-D-erythritol synthase homolog
    isoprenoid synthase domain containing
    notch1-induced protein
    testicular tissue protein Li 97
    NP_001094887.1
    NP_001094896.1
    NP_001355126.1

    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_032690.2 RefSeqGene

      Range
      4785..338798
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001101417.4 → NP_001094887.1  D-ribitol-5-phosphate cytidylyltransferase isoform b

      See identical proteins and their annotated locations for NP_001094887.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC004741, AC006035, AC073629, AC079155
      UniProtKB/TrEMBL
      A0A140VJM1
      Related
      ENSP00000382249.3, ENST00000399310.3
      Conserved Domains (1) summary
      cd02516
      Location:47 → 223
      CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

    2. NM_001101426.4 → NP_001094896.1  D-ribitol-5-phosphate cytidylyltransferase isoform a

      See identical proteins and their annotated locations for NP_001094896.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC004741, AC006035, AC073629, AC079155
      UniProtKB/Swiss-Prot
      A4D126, A8MU35, H9KVB2
      Related
      ENSP00000385478.2, ENST00000407010.7
      Conserved Domains (1) summary
      cd02516
      Location:47 → 273
      CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

    3. NM_001368197.1 → NP_001355126.1  D-ribitol-5-phosphate cytidylyltransferase isoform c

      Status: REVIEWED

      Source sequence(s)
      AC004741, AC006035, AC073629, AC079155

    RNA

    1. NR_160656.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC004741, AC006035, AC073629, AC079155

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      16087525..16421538 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      16220757..16551280 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A4D126.2 GenPept UniProtKB/Swiss-Prot:A4D126

    Gene LinkOut

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

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