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
Disease Acronyms (UniProt) Disease acronyms from UniProt database	MDDGA7, MDDGC7
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(11)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005829	Component	Cytosol	IBA	21873635
GO:0005829	Component	Cytosol	IDA	26687144
GO:0007411	Process	Axon guidance	IEA
GO:0008299	Process	Isoprenoid biosynthetic process	IEA
GO:0035269	Process	Protein O-linked mannosylation	IBA	21873635
GO:0035269	Process	Protein O-linked mannosylation	IMP	22522420, 22522421
GO:0042803	Function	Protein homodimerization activity	IDA	26687144
GO:0047349	Function	D-ribitol-5-phosphate cytidylyltransferase activity	IBA	21873635
GO:0047349	Function	D-ribitol-5-phosphate cytidylyltransferase activity	IDA	26687144
GO:0070567	Function	Cytidylyltransferase activity	IBA	21873635
GO:0070567	Function	Cytidylyltransferase activity	IDA	26687144

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 (28)

Disease term	Disease name	dbSNP ID	References
Causal
Agenesis of corpus callosum	Agenesis of corpus callosum	rs754914260, rs1057519053, rs1057519056, rs1057519054, rs1057519055, rs1057519057, rs1384496494, rs1599017933
Anterior segment dysgenesis	Irido-corneo-trabecular dysgenesis (disorder)	rs121907917, rs72549387, rs121909248, rs104893861, rs104893862, rs80358194, rs2113111009, rs104893957, rs104893958, rs104893954, rs587778873, rs587778874, rs878853070, rs752281590, rs369858688 View all (8 more)
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322 View all (150 more)
Congenital hydrocephalus	Congenital Hydrocephalus	rs387907321, rs1575362239, rs1576408050, rs1576412227, rs1576426439, rs1588574984, rs1588622713	22522421
Congenital muscular dystrophy	Congenital muscular dystrophy (disorder)	rs1565627745, rs774985604, rs1565629479, rs121913572, rs121913575, rs121913576, rs58932704, rs58912633, rs121912495, rs121912496, rs60458016, rs387906881, rs750764003, rs387907068, rs786205117 View all (45 more)	23288328
Congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies	MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 8	rs119463990, rs587777813, rs398123555, rs119463996, rs587777748, rs119463991, rs119463992, rs119464997, rs267606814, rs119463989, rs533916138, rs587777815, rs200198778, rs267606969, rs267606963 View all (138 more)
Cryptorchidism	Cryptorchidism	rs121912555, rs104894697, rs104894698, rs398122886
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Glaucoma	Glaucoma	rs121918355, rs1566660365, rs1566635134, rs121918356, rs1566634475, rs28936700, rs55771538, rs28936701, rs104893622, rs55989760, rs72549387, rs104893628, rs2125316417, rs104893629, rs74315328 View all (29 more)
Hydrocephalus	Hydrocephalus	rs387907320, rs369384363, rs387907321, rs372127610, rs770273135, rs797045095, rs797045707, rs769795916, rs781251438, rs922703465, rs376078512, rs1567043467, rs1587149916, rs1586841546	22522421
Limb-girdle muscular dystrophy-dystroglycanopathy	ISPD-related limb-girdle muscular dystrophy R20, MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 7	rs374042455, rs1559414655	2328832, 23288328, 2522420, 23390185, 22522420, 22522421, 27234031, 26687144
Limb-girdle muscular dystrophy	Muscular Dystrophies, Limb-Girdle, MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K	rs2137534216, rs104894422, rs762777463, rs104894423, rs137854524, rs137854521, rs137854523, rs137854529, rs398123555, rs119463996, rs587777814, rs119463992, rs267606971, rs267606967, rs28941782 View all (762 more)	23288328, 22522420, 22522421
Macrocephaly	Macrocephaly	rs786204854, rs764333096, rs1557739557
Mental retardation	Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)
Microcephaly	Microcephaly	rs397704721, rs267607176, rs267607177, rs397704725, rs267606717, rs267606718, rs199422202, rs121434311, rs199422203, rs199422126, rs387906274, rs121434305, rs199422125, rs199422135, rs189678019 View all (280 more)
Microphthalmos	Microphthalmos	rs794726862, rs1329285216
Muscle eye brain disease	Muscle eye brain disease	rs193919335, rs386834017, rs28940869, rs193919336, rs267606962, rs386834035, rs386834012, rs386834013, rs386834015, rs138642840, rs386834016, rs386834018, rs386834019, rs386834020, rs386834021 View all (51 more)	22522421, 22522420
Muscular dystrophy	Muscular Dystrophy	rs200198778, rs121908110, rs121908185, rs58932704, rs61672878, rs60458016, rs387906881, rs397509417, rs267607644, rs267607634, rs59332535, rs797045898, rs755660222, rs142908436, rs886039913 View all (15 more)
Muscular dystrophy-dystroglycanopathy	MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 7, Muscular Dystrophy-Dystroglycanopathy (Congenital with Brain and Eye Anomalies) Type A, 1	rs193919336, rs386834035, rs104894682, rs28937901, rs28937902, rs28937903, rs28937904, rs121908110, rs121908675, rs397515396, rs397515397, rs387907160, rs387907161, rs387907162, rs368593151 View all (20 more)	23288328, 9492098, 22522420, 24120487, 22522421, 26687144, 2522420, 23217329, 2328832
Myopathy	Myopathy	rs137854521, rs386834236, rs121908557, rs121909092, rs111033570, rs104894299, rs104894294, rs121909273, rs121909274, rs121909275, rs199474699, rs199476140, rs118192165, rs118192169, rs118192166 View all (81 more)	22522421
Hypotonia	Neonatal Hypotonia	rs141138948, rs397517172, rs869312824, rs1583169151
Optic atrophy	Optic Atrophy	rs121434508, rs267607017, rs80356524, rs80356525, rs879255560, rs104893753, rs80356529, rs397515360, rs104893620, rs199476104, rs199476112, rs199476118, rs398124298, rs770066665, rs398124299 View all (37 more)
Persistent hyperplastic primary vitreous	Persistent Hyperplastic Primary Vitreous	rs587777664, rs587777666, rs878853243
Polymicrogyria	Polymicrogyria	rs1558010146, rs1558003446, rs1575508937
Retinal detachment	Retinal Detachment	rs1555976049, rs1592230091
Retinal dystrophy	Retinal Dystrophies	rs267606794, rs200691042, rs397704718, rs202193201, rs794728002, rs121965036, rs121965057, rs121918129, rs137853190, rs386834252, rs121918165, rs137853113, rs137853114, rs121918328, rs587777803 View all (2328 more)
Syndromic microphthalmia	Anophthalmos	rs786205873, rs104894464, rs786205874, rs104894465, rs387906701, rs1566623121, rs786205879, rs1566624472, rs397514463, rs1566623392, rs387907252, rs397518481, rs397518482, rs397518483, rs587776457 View all (19 more)
Walker-warburg congenital muscular dystrophy	Walker-Warburg congenital muscular dystrophy	rs119463990, rs587777813, rs398123555, rs587777748, rs119463991, rs119463992, rs119464997, rs267606814, rs104894679, rs104894680, rs104894682, rs28937901, rs28937903, rs28937905, rs104894691 View all (69 more)	22522420, 22522421, 24120487

Show/Hide Unknown Diseases (6)

Disease term	Disease name	Source
Unknown
Specific learning disorder	Specific learning disability	ClinVar
Congenital Muscular Dystrophy Without Intellectual Disability	congenital muscular dystrophy without intellectual disability	GenCC
Metabolic Syndrome	Metabolic Syndrome	GWAS
Diabetes	Diabetes	GWAS
Carpal Tunnel Syndrome	Carpal Tunnel Syndrome	GWAS
Ischemic Stroke	Ischemic Stroke	GWAS

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text Mining
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)