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

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	729920
Gene name	CDP-L-ribitol pyrophosphorylase A
Gene symbol	CRPPA
Synonyms (NCBI Gene)	ISPDLGMDR20MDDGA7MDDGC7NiphISPD
Chromosome	7
Chromosome location	7p21.2
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]

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

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

1023

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive limb-girdle muscular dystrophy type 2U	Pathogenic; Likely pathogenic	rs370499190, rs2128321525, rs587777797, rs587777798, rs2128321527, rs1157302803, rs2546759145, rs2546759287, rs1420940583, rs1418861315, rs886041302, rs370627877, rs767978961, rs748007203, rs2546652810 View all (13 more)	RCV001390079 RCV002471170 RCV000144515 RCV000144516 RCV002238368 RCV003051155 RCV002770214 RCV002967035 RCV002982638 RCV003047070 RCV000650388 RCV002229838 RCV000548174 RCV003787526 RCV003788266 RCV003792466 RCV000650387 RCV005222703 RCV002525923 RCV000532194 RCV000706360 RCV000813269 RCV000793995 RCV002549285 RCV001234441 RCV001226801 RCV001232279 RCV001228819
Congenital muscular dystrophy due to integrin alpha-7 deficiency	Pathogenic	rs1554320168	RCV000626153
CRPPA-related disorder	Likely pathogenic	rs776803163	RCV003314258
ISPD-related disorder	Pathogenic	rs370627877	RCV000844945
Muscular dystrophy-dystroglycanopathy	Pathogenic	rs1554371369	RCV000500653
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7	Pathogenic; Likely pathogenic	rs370499190, rs2128422954, rs587777798, rs2128321527, rs2546749179, rs1157302803, rs2546759145, rs2546759287, rs1420940583, rs1418861315, rs886041302, rs370627877, rs886042554, rs767978961, rs748007203 View all (22 more)	RCV001390079 RCV001844361 RCV002228673 RCV002238368 RCV002471798 RCV003051155 RCV002770214 RCV002967035 RCV002982638 RCV003047070 RCV000650388 RCV002229838 RCV001330286 RCV000548174 RCV003787526 RCV003788266 RCV003792466 RCV003883224 RCV000024269 RCV000024271 RCV000024273 RCV000024274 RCV000024275 RCV000024276 RCV002525923 RCV000532194 RCV000032809 RCV000032811 RCV000032813 RCV000706360 RCV000813269 RCV000793995 RCV002549285 RCV001234441 RCV001226801 RCV001232279 RCV001228819
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8	Likely pathogenic; Pathogenic	rs587777798	RCV000714703

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Uncertain significance; Benign	rs142712241, rs1295127, rs146329563	RCV005899187 RCV005905749 RCV005913994
Cervical cancer	Benign	rs1918859	RCV005899188
Cholangiocarcinoma	Likely benign; Benign	rs75231577, rs1295127	RCV005917803 RCV005905751
Congenital Muscular Dystrophy, alpha-dystroglycan related	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs141625803, rs192925278, rs61734789, rs7782939, rs61746966, rs558064127, rs3839757, rs114363936, rs181099904, rs185594460, rs142647500, rs6461252, rs16878689, rs376909665, rs202108204 View all (189 more)	RCV000403197 RCV001162751 RCV000380541 RCV000347035 RCV000363271 RCV000292121 RCV000272252 RCV001164711 RCV001162651 RCV000303108 RCV000333361 RCV000280181 RCV000297186 RCV001164709 RCV001159796 RCV001161197 RCV001164710 RCV000285781 RCV000374609 RCV001164713 RCV000362747 RCV000322871 RCV000379843 RCV000351869 RCV000403144 RCV000404980 RCV000291176 RCV000298367 RCV000276163 RCV000333641 RCV000376539 RCV000379920 RCV000313485 RCV000321245 RCV000392061 RCV000303904 RCV000263080 RCV000333534 RCV000295114 RCV000350002 RCV000342731 RCV000308621 RCV000319984 RCV000370795 RCV000308021 RCV000281827 RCV000386488 RCV000294677 RCV000360875 RCV000298003 RCV000275452 RCV000332893 RCV000389680 RCV000344945 RCV000383139 RCV000339211 RCV000304125 RCV000355608 RCV000322941 RCV000278427 RCV000335784 RCV000348445 RCV000404602 RCV000307607 RCV000365371 RCV000273075 RCV000267318 RCV000279803 RCV000344564 RCV000339125 RCV000259452 RCV000298175 RCV000385829 RCV000282103 RCV000337055 RCV000335268 RCV000406561 RCV000357924 RCV000265546 RCV000348239 RCV000354647 RCV000262687 RCV000288402 RCV000342617 RCV000362674 RCV000271549 RCV000359606 RCV000324856 RCV000293172 RCV000309893 RCV000329915 RCV000276090 RCV000391144 RCV000274708 RCV000271470 RCV000310200 RCV000259384 RCV000373988 RCV000309566 RCV000347948 RCV000303777 RCV000268563 RCV000320144 RCV000386326 RCV000392455 RCV000403384 RCV000394395 RCV000311300 RCV000368418 RCV000328895 RCV000284387 RCV000393099 RCV000281756 RCV000370461 RCV000403935 RCV000372521 RCV000319044 RCV000375968 RCV000392053 RCV000350477 RCV000296543 RCV000406091 RCV000361195 RCV000355411 RCV000386863 RCV000381165 RCV000357657 RCV000268872 RCV000387775 RCV000340702 RCV000393577 RCV001164714 RCV001164712 RCV001161098 RCV001161196 RCV001162650 RCV001162153 RCV001162154 RCV001164180 RCV001164181 RCV001164182 RCV001164183 RCV001159279 RCV001159280 RCV001159281 RCV001159282 RCV001159283 RCV001159284 RCV001160639 RCV001160640 RCV001162255 RCV001162256 RCV001162257 RCV001164285 RCV001164286 RCV001164287 RCV001164288 RCV001159371 RCV001159372 RCV001159373 RCV001159374 RCV001160738 RCV001160739 RCV001160740 RCV001160741 RCV001160742 RCV001162357 RCV001162358 RCV001164400 RCV001164401 RCV001164402 RCV001164403 RCV001164404 RCV001164405 RCV001159460 RCV001159461 RCV001159462 RCV001159463 RCV001159464 RCV001159465 RCV001160831 RCV001162458 RCV001162459 RCV001164503 RCV001164504 RCV001164505 RCV001164506 RCV001164507 RCV001159571 RCV001159572 RCV001159573 RCV001159574 RCV001160955 RCV001160956 RCV001160957 RCV001160958 RCV001160959 RCV001162550 RCV001162551 RCV001164596 RCV001164597 RCV001164598 RCV001159685 RCV001159686 RCV001159687 RCV001161094 RCV001161095 RCV001161096 RCV001161097 RCV001162649 RCV001159795 RCV001162648
Lung cancer	Benign	rs1295127	RCV005905752
Melanoma	Uncertain significance	rs547473863	RCV005895891
Ovarian serous cystadenocarcinoma	Likely benign; Benign	rs75231577, rs1295127	RCV005917801 RCV005905750
Sarcoma	Benign	rs1918859	RCV005899189
Thymoma	Likely benign; Benign	rs75231577, rs1918859	RCV005917802 RCV005899191
Uterine carcinosarcoma	Benign	rs1918859	RCV005899190

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)