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

Gene ID: 729920, updated on 23-Nov-2023

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
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Genomic context

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See CRPPA in Genome Data Viewer
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

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