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ISPD isoprenoid synthase domain containing [ Homo sapiens (human) ]

Gene ID: 729920, updated on 25-Jul-2018

Summary

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Official Symbol
ISPDprovided by HGNC
Official Full Name
isoprenoid synthase domain containingprovided by HGNC
Primary source
HGNC:HGNC:37276
See related
Ensembl:ENSG00000214960 MIM:614631; Vega:OTTHUMG00000152447
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; hISPD; MDDGA7; MDDGC7; hCG_1745121
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

Genomic context

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See ISPD in Genome Data Viewer
Location:
7p21.2
Exon count:
22
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (16087527..16502500, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (16127152..16460947, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927558 Neighboring gene uncharacterized LOC105375167 Neighboring gene uncharacterized LOC107986725 Neighboring gene ribosomal protein L36a pseudogene 29 Neighboring gene ISPD antisense RNA 1 Neighboring gene uncharacterized LOC105375168 Neighboring gene sclerostin domain containing 1 Neighboring gene leucine rich repeat containing 72 Neighboring gene ataxin 2 like pseudogene

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 Jun 15 11:32:44 2016

Bibliography

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Related articles in PubMed

  1. Recent advancements in understanding mammalian O-mannosylation. Sheikh MO, et al. Glycobiology, 2017 Sep 1. PMID 28810660, Free PMC Article
  2. 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
  3. 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
  4. A novel homozygous ISPD gene mutation causing phenotype variability in a consanguineous family. Baranello G, et al. Neuromuscul Disord, 2015 Jan. PMID 25444434
  5. Limb-girdle muscular dystrophy with α-dystroglycan deficiency and mutations in the ISPD gene. Tasca G, et al. Neurology, 2013 Mar 5. PMID 23390185

See all (22) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of alpha-dystroglycan.
    Title: Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of α-dystroglycan.
  9. ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome.
    Title: ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome.
  10. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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

NHGRI GWAS Catalog

Description
Impact of four loci on serum tamsulosin hydrochloride concentration.
NHGRI GWA 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 BioSystems

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General gene information

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Markers

Homology

Clone Names

  • FLJ42815

Gene Ontology Provided by GOA

Function Evidence Code Pubs
D-ribitol-5-phosphate cytidylyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
D-ribitol-5-phosphate cytidylyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
cytidylyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytidylyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
axon guidance IEA
Inferred from Electronic Annotation
more info
  
isoprenoid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
protein O-linked mannosylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein O-linked mannosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
notch1-induced protein
testicular tissue protein Li 97
NP_001094887.1
NP_001094896.1
XP_006715833.1
XP_011513801.1
XP_011513802.1
XP_011513803.1
XP_011513810.1
XP_011513811.1
XP_016868064.1
XP_016868065.1
XP_016868066.1
XP_016868067.1
XP_024302677.1
XP_024302678.1
XP_024302679.1
XP_024302680.1

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_032690.1 RefSeqGene

    Range
    5001..338796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001101417.3 → 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/Swiss-Prot
    A4D126
    UniProtKB/TrEMBL
    A0A140VJM1
    Related
    ENSP00000382249.3, OTTHUMP00000201709, ENST00000399310.3, OTTHUMT00000326299
    Conserved Domains (1) summary
    cd02516
    Location:47 → 223
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

  2. NM_001101426.3 → 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 longer isoform (a).
    Source sequence(s)
    AC004741, AC006035, AC073629, AC079155
    UniProtKB/Swiss-Prot
    A4D126
    Related
    ENSP00000385478.2, OTTHUMP00000201687, ENST00000407010.6, OTTHUMT00000326252
    Conserved Domains (1) summary
    cd02516
    Location:47 → 273
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    16087527..16502500 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446910.1 → XP_024302678.1  D-ribitol-5-phosphate cytidylyltransferase isoform X6

    Conserved Domains (1) summary
    cl11394
    Location:1 → 172
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  2. XM_024446911.1 → XP_024302679.1  D-ribitol-5-phosphate cytidylyltransferase isoform X8

    Conserved Domains (1) summary
    cl11394
    Location:1 → 159
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  3. XM_024446909.1 → XP_024302677.1  D-ribitol-5-phosphate cytidylyltransferase isoform X6

    Conserved Domains (1) summary
    cl11394
    Location:1 → 172
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  4. XM_011515508.2 → XP_011513810.1  D-ribitol-5-phosphate cytidylyltransferase isoform X6

    See identical proteins and their annotated locations for XP_011513810.1

    Conserved Domains (1) summary
    cl11394
    Location:1 → 172
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  5. XM_011515500.2 → XP_011513802.1  D-ribitol-5-phosphate cytidylyltransferase isoform X3

    Conserved Domains (1) summary
    cd02516
    Location:47 → 260
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

  6. XM_006715770.3 → XP_006715833.1  D-ribitol-5-phosphate cytidylyltransferase isoform X4

    Conserved Domains (1) summary
    cd02516
    Location:4 → 190
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

  7. XM_011515509.2 → XP_011513811.1  D-ribitol-5-phosphate cytidylyltransferase isoform X6

    See identical proteins and their annotated locations for XP_011513811.1

    Conserved Domains (1) summary
    cl11394
    Location:1 → 172
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  8. XM_017012577.1 → XP_016868066.1  D-ribitol-5-phosphate cytidylyltransferase isoform X10

  9. XM_017012578.1 → XP_016868067.1  D-ribitol-5-phosphate cytidylyltransferase isoform X11

  10. XM_017012575.1 → XP_016868064.1  D-ribitol-5-phosphate cytidylyltransferase isoform X1

  11. XM_011515499.2 → XP_011513801.1  D-ribitol-5-phosphate cytidylyltransferase isoform X2

    Conserved Domains (1) summary
    cd02516
    Location:47 → 273
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

  12. XM_017012576.1 → XP_016868065.1  D-ribitol-5-phosphate cytidylyltransferase isoform X7

  13. XM_011515501.2 → XP_011513803.1  D-ribitol-5-phosphate cytidylyltransferase isoform X5

    Conserved Domains (1) summary
    cd02516
    Location:47 → 273
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

  14. XM_024446912.1 → XP_024302680.1  D-ribitol-5-phosphate cytidylyltransferase isoform X9

    Conserved Domains (1) summary
    cd02516
    Location:4 → 190
    CDP-ME_synthetase; CDP-ME synthetase is involved in mevalonate-independent isoprenoid production

RNA

  1. XR_001744868.1 RNA Sequence

  2. XR_001744866.1 RNA Sequence

  3. XR_001744864.1 RNA Sequence

  4. XR_001744865.1 RNA Sequence

  5. XR_001744867.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A4D126.2 GenPept UniProtKB/Swiss-Prot:A4D126

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