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.	10329
Gene name Gene Name - the full gene name approved by the HGNC.	Ribitol xylosyltransferase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	RXYLT1
Synonyms (NCBI Gene) Gene synonyms aliases	HP10481, MDDGA10, TMEM5
Chromosome Chromosome number	12
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	12q14.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a type II transmembrane protein that is thought to have glycosyltransferase function. Mutations in this gene result in cobblestone lissencephaly. Alternative splicing results in multiple transcript variants encoding different isoforms. [

Show/Hide all(14)

SNP ID	Visualize variation	Clinical significance	Consequence
rs73122634	C>T	Benign-likely-benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, missense variant
rs141095352	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, 5 prime UTR variant, non coding transcript variant, synonymous variant, coding sequence variant
rs397514543	G>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs397514546	A>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs397514696	G>-	Pathogenic	Genic upstream transcript variant, non coding transcript variant, 5 prime UTR variant, frameshift variant, coding sequence variant, upstream transcript variant
rs745327804	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, 5 prime UTR variant, missense variant, non coding transcript variant
rs748590408	GGGCCTCAGGAAGGGGGCGGCCCCCGCG>-	Likely-pathogenic, pathogenic	Coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, frameshift variant, non coding transcript variant, upstream transcript variant
rs778174763	G>A	Likely-pathogenic	Splice donor variant
rs886039490	G>-	Pathogenic	5 prime UTR variant, non coding transcript variant, frameshift variant, genic upstream transcript variant, upstream transcript variant, coding sequence variant
rs948674144	A>-	Pathogenic	5 prime UTR variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1303817555	->G	Likely-pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant, non coding transcript variant
rs1354951198	T>-	Pathogenic-likely-pathogenic	Frameshift variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs1565898123	G>-	Likely-pathogenic	Splice acceptor variant
rs1565899712	G>A	Likely-pathogenic	Non coding transcript variant, stop gained, 5 prime UTR variant, coding sequence variant

Show/Hide all(18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0005515	Function	Protein binding	IPI	27601598, 28514442, 29477842, 32296183, 32814053, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IDA	25279699, 29477842
GO:0005794	Component	Golgi apparatus	IEA
GO:0005886	Component	Plasma membrane	TAS	10072769
GO:0006486	Process	Protein glycosylation	IEA
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IBA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IDA	27130732, 27733679
GO:0035269	Process	Protein O-linked glycosylation via mannose	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IMP	25279699
GO:0120053	Function	Ribitol beta-1,4-xylosyltransferase activity	IBA
GO:0120053	Function	Ribitol beta-1,4-xylosyltransferase activity	IDA	27733679, 29477842
GO:0120053	Function	Ribitol beta-1,4-xylosyltransferase activity	IEA
GO:0120053	Function	Ribitol beta-1,4-xylosyltransferase activity	TAS	27130732

MIM	HGNC	e!Ensembl
605862	13530	ENSG00000118600

Protein

UniProt ID

Q9Y2B1

Protein name

Ribitol-5-phosphate xylosyltransferase 1 (EC 2.4.2.61) (Transmembrane protein 5) (UDP-D-xylose:ribitol-5-phosphate beta1,4-xylosyltransferase)

Protein function

Acts as a UDP-D-xylose:ribitol-5-phosphate beta1,4-xylosyltransferase, which catalyzes the transfer of UDP-D-xylose to ribitol 5-phosphate (Rbo5P) to form the Xylbeta1-4Rbo5P linkage on O-mannosyl glycan (Probable) (PubMed:27733679, PubMed:29477

Family and domains

Sequence

MRLTRKRLCSFLIALYCLFSLYAAYHVFFGRRRQAPAGSPRGLRKGAAPARERRGREQST
LESEEWNPWEGDEKNEQQHRFKTSLQILDKSTKGKTDLSVQIWGKAAIGLYLWEHIFEGL
LDPSDVTAQWREGKSIVGRTQYSFITGPAVIPGYFSVDVNNVVLILNGREKAKIFYATQW
LLYAQNLVQIQKLQHLAVVLLGNEHCDNEWINPFLKRNGGFVELLFIIYDSPWINDVDVF
QWPLGVATYRNFPVVEASWSMLHDERPYLCNFLGTIYENSSRQALMNILKKDGNDKLCWV
SAREHWQPQETNESLKNYQDALLQSDLTLCPVGVNTECYRIYEACSYGSIPVVEDVMTAG
NCGNTSVHHGAPLQLLKSMGAPFIFIKNWKELPAVLEKEKTIILQEKIERRKMLLQWYQH
FKTELKMKFTNILESSFLMNNKS

Sequence length

443

Interactions

View interactions

	KEGG
	Mannose type O-glycan biosynthesis Metabolic pathways

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10	rs397514546, rs397514695, rs397514696, rs1565899712, rs397514543, rs150736997, rs397514545	N/A
Walker-Warburg Congenital Muscular Dystrophy	walker-warburg congenital muscular dystrophy	rs397514695, rs150736997	N/A

Show/Hide Unknown Diseases (3)

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.
Cleft Lip With Or Without Cleft Palate	Cleft lip with or without cleft palate	N/A	N/A	GWAS
Muscle Eye Brain Disease	muscle-eye-brain disease	N/A	N/A	GenCC
Muscular dystrophy	muscular dystrophy-dystroglycanopathy, type A	N/A	N/A	GenCC

Show/Hide Text Mining Associations (10)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Brain Diseases	Associate	27212206
Cobblestone Lissencephaly	Associate	23217329
Cochlear Diseases	Associate	27212206
Craniometaphyseal Dysplasia Autosomal Dominant	Associate	27212206
Gonadal Dysgenesis	Associate	23217329
Intellectual Disability	Associate	27212206
Muscular Dystrophies Limb Girdle	Associate	27212206
Neural Tube Defects	Associate	23217329
Polymicrogyria	Associate	27212206
Walker Warburg Syndrome	Associate	27212206, 27733679, 36007194

RXYLT1 (ribitol xylosyltransferase 1)