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	10329
Gene name	Ribitol xylosyltransferase 1
Gene symbol	RXYLT1
Synonyms (NCBI Gene)	HP10481MDDGA10TMEM5
Chromosome	12
Chromosome location	12q14.2
Summary	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

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10	Likely pathogenic; Pathogenic	rs199605239, rs1897640752, rs2500533538, rs886039490, rs2500486724, rs397514543, rs150736997, rs397514545, rs397514546, rs397514695, rs397514696, rs1565899712, rs1592838547	RCV002250302 RCV002282772 RCV002282775 RCV005630251 RCV005631220 View all (8 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Walker-Warburg congenital muscular dystrophy	Likely pathogenic; Pathogenic	rs150736997, rs397514695	RCV000611814 RCV004017340	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Familial cancer of breast	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUSCLE EYE BRAIN DISEASE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUSCLE-EYE-BRAIN DISEASE	—	ClinGen, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RXYLT1-related disorder	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WALKER-WARBURG SYNDROME	—	CTD, Orphanet CTD, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (54)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Absence of septum pellucidum	Absence Of Septum Pellucidum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
alpha-Dystroglycanopathies	alpha-Dystroglycanopathy	BEFREE	30017359		★★★★★ ★☆☆☆☆ Found in Text Mining only
alpha-Dystroglycanopathies	alpha-Dystroglycanopathy	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Anophthalmos	Syndromic microphthalmia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	27212206	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cobblestone Lissencephaly	Cobblestone Lissencephaly	BEFREE	23217329		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cobblestone Lissencephaly	Cobblestone lissencephaly	Pubtator	23217329	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cobblestone Lissencephaly	Cobblestone Lissencephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cochlear Diseases	Cochlear diseases	Pubtator	27212206	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	28484880		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Craniometaphyseal Dysplasia Autosomal Dominant	Craniometaphyseal dysplasia	Pubtator	27212206	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Fukuyama Type Congenital Muscular Dystrophy	Fukuyama Type Congenital Muscular Dystrophy	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Gonadal Dysgenesis	Gonadal dysgenesis	Pubtator	23217329	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gonadal Dysgenesis	Gonadal Dysgenesis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	27212206	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscle eye brain disease	Muscle Eye Brain Disease	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Muscular Dystrophy	Muscular dystrophy	BEFREE	27733679		★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K	Limb-girdle muscular dystrophy	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy-Dystroglycanopathy (Congenital with Brain and Eye Anomalies) Type A, 1	Muscular Dystrophy-Dystroglycanopathy	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 10	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	GENOMICS_ENGLAND_DG	23217329, 23519211, 27212206		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 10	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	CLINVAR_DG	23217329, 23519211		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 10	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	UNIPROT_DG	23217329, 23519211, 27130732, 27212206, 27733679		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neural Tube Defects	Neural Tube Defect	BEFREE	23217329		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural tube defect	Pubtator	23217329	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	Pubtator	27212206	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Detachment	Retinal Detachment	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Dysplasia	Retinal Dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Submucous cleft of hard palate	Submucosal cleft palate	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	ORPHANET_DG	23217329, 23519211		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	CLINVAR_DG	23217329		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	CTD_human_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Walker-Warburg syndrome	Walker-Warburg Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

RXYLT1 (ribitol xylosyltransferase 1)