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Aliases for RXYLT1 Gene

Aliases for RXYLT1 Gene

  • Ribitol Xylosyltransferase 1 2 3 5
  • Transmembrane Protein 5 2 3 4
  • UDP-D-Xylose:Ribitol-5-Phosphate Beta1,4-Xylosyltransferase 3 4
  • TMEM5 3 4
  • Ribitol-5-Phosphate Xylosyltransferase 1 3
  • Type II Membrane Protein 3
  • EC 2.4.2.- 4
  • HP10481 3
  • MDDGA10 3

External Ids for RXYLT1 Gene

Previous HGNC Symbols for RXYLT1 Gene

  • TMEM5

Summaries for RXYLT1 Gene

Entrez Gene Summary for RXYLT1 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. [provided by RefSeq, May 2013]

GeneCards Summary for RXYLT1 Gene

RXYLT1 (Ribitol Xylosyltransferase 1) is a Protein Coding gene. Diseases associated with RXYLT1 include Muscular Dystrophy-Dystroglycanopathy , Type A, 10 and Walker-Warburg Syndrome. Among its related pathways are Mannose type O-glycan biosynthesis and Metabolism.

UniProtKB/Swiss-Prot for RXYLT1 Gene

  • UDP-xylosyltransferase involved in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity (PubMed:25279699, PubMed:27130732, PubMed:27733679, PubMed:27601598). 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 (PubMed:27130732, PubMed:27733679).

Additional gene information for RXYLT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RXYLT1 Gene

Genomics for RXYLT1 Gene

GeneHancer (GH) Regulatory Elements for RXYLT1 Gene

Promoters and enhancers for RXYLT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J063779 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 655.5 +0.4 379 1.9 PKNOX1 CLOCK ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B E2F8 RXYLT1 PABPC1P4 LOC100420899 ENSG00000249753
GH12J063798 Promoter 0.5 EPDnew 650.4 +18.3 18342 0.1 RXYLT1 ENSG00000249753 PABPC1P4
GH12J062933 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.6 -845.3 -845271 2.9 PKNOX1 CLOCK SMAD1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ENSG00000252660 GC12P062936 PPM1H MON2 ENSG00000257354 RXYLT1 RNU1-83P GC12M062851
GH12J063420 Enhancer 0.9 ENCODE 9.7 -359.4 -359447 0.2 PKNOX1 FEZF1 ZNF2 YY1 TCF12 CBX5 ZNF143 KLF13 REST TSHZ1 RXYLT1 GC12M063412 ENSG00000258117
GH12J063814 Enhancer 0.6 ENCODE 5 +35.0 35029 1.1 TRIM22 JUNB ELF1 RELA SP1 IKZF1 RUNX3 IKZF2 RXYLT1 PABPC1P4 RXYLT1-AS1 ENSG00000249753
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RXYLT1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RXYLT1 Gene

Genomic Locations for RXYLT1 Gene
chr12:63,779,803-63,809,558
(GRCh38/hg38)
Size:
29,756 bases
Orientation:
Plus strand
chr12:64,173,583-64,203,338
(GRCh37/hg19)
Size:
29,756 bases
Orientation:
Plus strand

Genomic View for RXYLT1 Gene

Genes around RXYLT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RXYLT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RXYLT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RXYLT1 Gene

Proteins for RXYLT1 Gene

  • Protein details for RXYLT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2B1-RXLT1_HUMAN
    Recommended name:
    Ribitol-5-phosphate xylosyltransferase 1
    Protein Accession:
    Q9Y2B1
    Secondary Accessions:
    • A8K017
    • Q6PKD6

    Protein attributes for RXYLT1 Gene

    Size:
    443 amino acids
    Molecular mass:
    51146 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH02596.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

neXtProt entry for RXYLT1 Gene

Post-translational modifications for RXYLT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RXYLT1 Gene

No data available for DME Specific Peptides for RXYLT1 Gene

Domains & Families for RXYLT1 Gene

Gene Families for RXYLT1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RXYLT1 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for RXYLT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y2B1

UniProtKB/Swiss-Prot:

RXLT1_HUMAN :
  • Belongs to the RXYLT1 family.
Family:
  • Belongs to the RXYLT1 family.
genes like me logo Genes that share domains with RXYLT1: view

Function for RXYLT1 Gene

Molecular function for RXYLT1 Gene

UniProtKB/Swiss-Prot Function:
UDP-xylosyltransferase involved in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity (PubMed:25279699, PubMed:27130732, PubMed:27733679, PubMed:27601598). 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 (PubMed:27130732, PubMed:27733679).

Enzyme Numbers (IUBMB) for RXYLT1 Gene

Gene Ontology (GO) - Molecular Function for RXYLT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0120053 ribitol beta-1,4-xylosyltransferase activity TAS 27130732
genes like me logo Genes that share ontologies with RXYLT1: view
genes like me logo Genes that share phenotypes with RXYLT1: view

Human Phenotype Ontology for RXYLT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for RXYLT1

miRNA for RXYLT1 Gene

miRTarBase miRNAs that target RXYLT1

Clone Products

No data available for Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for RXYLT1 Gene

Localization for RXYLT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RXYLT1 Gene

Golgi apparatus membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RXYLT1 gene
Compartment Confidence
plasma membrane 5
nucleus 5
golgi apparatus 5
extracellular 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RXYLT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IEA,IDA 25279699
GO:0005887 integral component of plasma membrane TAS 10072769
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with RXYLT1: view

Pathways & Interactions for RXYLT1 Gene

genes like me logo Genes that share pathways with RXYLT1: view

Pathways by source for RXYLT1 Gene

2 KEGG pathways for RXYLT1 Gene

UniProtKB/Swiss-Prot Q9Y2B1-RXLT1_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Interacting Proteins for RXYLT1 Gene

Selected Interacting proteins: Q9Y2B1-RXLT1_HUMAN for RXYLT1 Gene via IID

Symbol External ID(s) Details
GPR3

Gene Ontology (GO) - Biological Process for RXYLT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006486 protein glycosylation IEA --
GO:0035269 protein O-linked mannosylation IMP 25279699
genes like me logo Genes that share ontologies with RXYLT1: view

No data available for SIGNOR curated interactions for RXYLT1 Gene

Drugs & Compounds for RXYLT1 Gene

No Compound Related Data Available

Transcripts for RXYLT1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RXYLT1 Gene

No ASD Table

Relevant External Links for RXYLT1 Gene

GeneLoc Exon Structure for
RXYLT1
ECgene alternative splicing isoforms for
RXYLT1

Expression for RXYLT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RXYLT1 Gene:

RXYLT1

Evidence on tissue expression from TISSUES for RXYLT1 Gene

  • Adrenal gland(4.2)
  • Skin(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RXYLT1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pituitary gland
  • skull
  • tongue
Thorax:
  • breast
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
Pelvis:
  • anus
  • ovary
  • pelvis
  • penis
  • prostate
  • rectum
  • testicle
  • ureter
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • vertebrae
No Expression Related Data Available

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for RXYLT1 Gene

Orthologs for RXYLT1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RXYLT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMEM5 34 33
  • 99.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TMEM5 34 33
  • 88.26 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tmem5 33
  • 85.82 (n)
mouse
(Mus musculus)
Mammalia Tmem5 16 34 33
  • 85.67 (n)
dog
(Canis familiaris)
Mammalia TMEM5 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TMEM5 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMEM5 34 33
  • 73.17 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TMEM5 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tmem5 33
  • 61.27 (n)
Str.15588 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.29709 33
zebrafish
(Danio rerio)
Actinopterygii tmem5 34 33
  • 56.52 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
OneToOne
Species where no ortholog for RXYLT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RXYLT1 Gene

ENSEMBL:
Gene Tree for RXYLT1 (if available)
TreeFam:
Gene Tree for RXYLT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RXYLT1: view image

Paralogs for RXYLT1 Gene

No data available for Paralogs for RXYLT1 Gene

Variants for RXYLT1 Gene

Sequence variations from dbSNP and Humsavar for RXYLT1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs114036100 conflicting-interpretations-of-pathogenicity, benign, not specified, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 63,802,131(+) G/A 5_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs114694892 likely-benign, benign, not specified, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 63,781,143(+) C/T 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs115076664 likely-benign, benign, not specified, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 63,805,315(+) G/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs141095352 conflicting-interpretations-of-pathogenicity, benign, not specified, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 63,781,101(+) C/T 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs141536395 benign, not specified, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 63,808,986(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RXYLT1 Gene

Variant ID Type Subtype PubMed ID
nsv832441 CNV loss 17160897
nsv746 CNV deletion 18451855
nsv1046836 CNV gain 25217958
esv3629762 CNV loss 21293372
esv2759905 CNV gain 17122850
esv2751110 CNV gain 17911159

Variation tolerance for RXYLT1 Gene

Residual Variation Intolerance Score: 54.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.61; 65.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RXYLT1 Gene

Human Gene Mutation Database (HGMD)
RXYLT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RXYLT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RXYLT1 Gene

Disorders for RXYLT1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for RXYLT1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
muscular dystrophy-dystroglycanopathy , type a, 10
  • mddga10
walker-warburg syndrome
  • hydrocephalus, agyria, and retinal dysplasia
muscular dystrophy-dystroglycanopathy
  • cmd due to dystroglycanopathy
lissencephaly
muscular dystrophy
  • muscular dystrophies
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

RXLT1_HUMAN
  • Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A10 (MDDGA10) [MIM:615041]: An autosomal recessive disorder characterized by congenital muscular dystrophy associated with cobblestone lissencephaly and other brain anomalies, eye malformations, profound mental retardation, and death usually in the first years of life. Included diseases are the more severe Walker-Warburg syndrome and the slightly less severe muscle-eye-brain disease. {ECO:0000269 PubMed:23217329, ECO:0000269 PubMed:23519211, ECO:0000269 PubMed:27130732, ECO:0000269 PubMed:27212206, ECO:0000269 PubMed:27733679}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RXYLT1

genes like me logo Genes that share disorders with RXYLT1: view

No data available for Genatlas for RXYLT1 Gene

Publications for RXYLT1 Gene

  1. The functional O-mannose glycan on α-dystroglycan contains a phospho-ribitol primed for matriglycan addition. (PMID: 27130732) Praissman JL … Wells L (eLife 2016) 2 3 4 58
  2. The Muscular Dystrophy Gene TMEM5 Encodes a Ribitol β1,4-Xylosyltransferase Required for the Functional Glycosylation of Dystroglycan. (PMID: 27733679) Manya H … Endo T (The Journal of biological chemistry 2016) 2 3 4 58
  3. Identification of mutations in TMEM5 and ISPD as a cause of severe cobblestone lissencephaly. (PMID: 23217329) Vuillaumier-Barrot S … Seta N (American journal of human genetics 2012) 2 3 4 58
  4. The glucuronyltransferase B4GAT1 is required for initiation of LARGE-mediated α-dystroglycan functional glycosylation. (PMID: 25279699) Willer T … Campbell KP (eLife 2014) 3 4 58
  5. Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry. (PMID: 23519211) Jae LT … Brummelkamp TR (Science (New York, N.Y.) 2013) 3 4 58

Products for RXYLT1 Gene

Sources for RXYLT1 Gene

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