Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	729920
Gene name Gene Name - the full gene name approved by the HGNC.	CDP-L-ribitol pyrophosphorylase A
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CRPPA
Synonyms (NCBI Gene) Gene synonyms aliases	ISPD, LGMDR20, MDDGA7, MDDGC7, Nip, hISPD
Chromosome Chromosome number	7
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	7p21.2
Summary Summary of gene provided in NCBI Entrez Gene.	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]

Show/Hide all(34)

SNP ID	Visualize variation	Clinical significance	Consequence
rs148054819	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant
rs186882839	A>G,T	Pathogenic	Non coding transcript variant, terminator codon variant, stop lost
rs201334104	A>G	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, intron variant
rs368593151	G>A	Pathogenic	Coding sequence variant, intron variant, stop gained
rs370627877	G>A,T	Pathogenic, uncertain-significance, not-provided	Missense variant, intron variant, coding sequence variant, non coding transcript variant, stop gained
rs376195897	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant
rs376411072	G>A	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant, intron variant
rs377582530	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs387907160	G>C,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, intron variant
rs387907161	T>A	Pathogenic	Coding sequence variant, intron variant, stop gained
rs387907162	C>G	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs397514547	C>G,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs397514548	T>A,C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, stop gained
rs397515397	A>C	Pathogenic	Splice donor variant, intron variant
rs397515398	AAT>-	Likely-pathogenic, pathogenic, uncertain-significance	Non coding transcript variant, inframe deletion, coding sequence variant
rs397515408	A>C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, intron variant
rs397515409	G>A,C	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, intron variant
rs532057629	T>C	Conflicting-interpretations-of-pathogenicity, likely-benign	Non coding transcript variant, synonymous variant, coding sequence variant, intron variant
rs558064127	T>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs587777797	C>A,G	Pathogenic, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs761842188	C>G,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs763209907	T>C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs767978961	C>G	Likely-pathogenic, pathogenic	Splice acceptor variant
rs773325665	A>G	Likely-pathogenic	Splice donor variant, intron variant
rs886041302	->A	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs886043573	T>A,C	Pathogenic	Missense variant, non coding transcript variant, initiator codon variant
rs1048457038	C>-	Pathogenic-likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1202301143	C>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1466053365	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, coding sequence variant
rs1466219701	G>T	Pathogenic	Intron variant, stop gained, coding sequence variant
rs1472549168	G>A,C	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant, non coding transcript variant
rs1554305719	TATCTTCTTCTGT>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554320168	A>-	Likely-pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1554371369	C>-,CC	Pathogenic, likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant

Show/Hide all(19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA	26687144
GO:0005829	Component	Cytosol	IEA
GO:0006486	Process	Protein glycosylation	IEA
GO:0006486	Process	Protein glycosylation	IEA
GO:0007411	Process	Axon guidance	IEA
GO:0008299	Process	Isoprenoid biosynthetic process	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IBA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IMP	22522420, 22522421
GO:0042803	Function	Protein homodimerization activity	IDA	26687144
GO:0047349	Function	D-ribitol-5-phosphate cytidylyltransferase activity	IBA
GO:0047349	Function	D-ribitol-5-phosphate cytidylyltransferase activity	IDA	26687144
GO:0047349	Function	D-ribitol-5-phosphate cytidylyltransferase activity	IEA
GO:0070567	Function	Cytidylyltransferase activity	IDA	26687144
GO:0070567	Function	Cytidylyltransferase activity	IEA

MIM	HGNC	e!Ensembl
614631	37276	ENSG00000214960

Protein

UniProt ID

A4D126

Protein name

D-ribitol-5-phosphate cytidylyltransferase (EC 2.7.7.40) (2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein) (Isoprenoid synthase domain-containing protein) (hISPD)

Protein function

Cytidylyltransferase required for protein O-linked mannosylation (PubMed:22522420, PubMed:22522421, PubMed:26687144, PubMed:26923585, PubMed:27130732, PubMed:27601598). Catalyzes the formation of CDP-ribitol nucleotide sugar from D-ribitol 5-pho

PDB

4CVH

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01128	IspD	47 → 279	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Family
PF18706	ISPD_C	283 → 451	D-ribitol-5-phosphate cytidylyltransferase C-terminal domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed, with high expression in brain. {ECO:0000269|PubMed:22522420}.

Sequence

MEAGPPGSARPAEPGPCLSGQRGADHTASASLQSVAGTEPGRHPQAVAAVLPAGGCGERM
GVPTPKQFCPILERPLISYTLQALERVCWIKDIVVAVTGENMEVMKSIIQKYQHKRISLV
EAGVTRHRSIFNGLKALAEDQINSKLSKPEVVIIHDAVRPFVEEGVLLKVVTAAKEHGAA
GAIRPLVSTVVSPSADGCLDYSLERARHRASEMPQAFLFDVIYEAYQQCSDYDLEFGTEC
LQLALKYCCTKAKLVEGSPDLWKVTYKRDLYAAESIIKERISQEICVVMDTEEDNKHVGH
LLEEVLKSELNHVKVTSEALGHAGRHLQQIILDQCYNFVCVNVTTSDFQETQKLLSMLEE
SSLCILYPVVVVSVHFLDFKLVPPSQKMENLMQIREFAKEVKERNILLYGLLISYPQDDQ
KLQESLRQGAIIIASLIKERNSGLIGQLLIA

Sequence length

451

Interactions

View interactions

	KEGG
	Pentose and glucuronate interconversions Mannose type O-glycan biosynthesis Metabolic pathways

Show/Hide Causal Diseases (5)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital muscular dystrophy	Congenital muscular dystrophy due to integrin alpha-7 deficiency	rs1554320168	N/A
Limb-girdle muscular dystrophy	Autosomal recessive limb-girdle muscular dystrophy type 2U	rs587777798, rs587777797	N/A
Muscular Dystrophy-Dystroglycanopathy	muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7	rs397515396, rs397515397, rs886042554, rs387907160, rs387907161, rs387907162, rs368593151, rs397515408, rs397514547, rs397514548	N/A
muscular dystrophy-dystroglycanopathy	Muscular dystrophy-dystroglycanopathy	rs1554371369	N/A
Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8	rs587777798	N/A

Show/Hide Unknown Diseases (6)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Carpal Tunnel Syndrome	Carpal tunnel syndrome	N/A	N/A	GWAS
Congenital Muscular Dystrophy Without Intellectual Disability	congenital muscular dystrophy without intellectual disability	N/A	N/A	GenCC
Diabetes	Type 2 diabetes	N/A	N/A	GWAS
Ischemic Stroke	Ischemic stroke	N/A	N/A	GWAS
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS
Myopathy	myopathy caused by variation in CRPPA	N/A	N/A	GenCC

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Brain Diseases	Associate	23288328
Carcinoma Renal Cell	Associate	26220087
Cerebrovascular Trauma	Associate	23217329
Cobblestone Lissencephaly	Associate	23217329
Muscular Dystrophies	Associate	23288328
Muscular Dystrophies Limb Girdle	Associate	23288328, 26404900
Neoplasms	Associate	24413564
Walker Warburg Syndrome	Associate	22522420, 23288328, 30060766

CRPPA (CDP-L-ribitol pyrophosphorylase A)