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RXYLT1 ribitol xylosyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 10329, updated on 22-Apr-2024

Summary

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Official Symbol
RXYLT1provided by HGNC
Official Full Name
ribitol xylosyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:13530
See related
Ensembl:ENSG00000118600 MIM:605862; AllianceGenome:HGNC:13530
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TMEM5; HP10481; MDDGA10
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. [provided by RefSeq, May 2013]
Expression
Ubiquitous expression in testis (RPKM 8.9), thyroid (RPKM 7.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q14.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (63779909..63809562)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (63758617..63788268)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (64173689..64203342)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene T-box 20 pseudogene Neighboring gene DPY19L2 LCR2 recombination region 1 Neighboring gene DPY19L2 LCR2 recombination region 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4614 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:64173754-64174029 Neighboring gene ribosomal protein S27 pseudogene 24 Neighboring gene RXYLT1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:64237485-64237986 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:64237987-64238486 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 4 Neighboring gene microRNA 10527 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:64264449-64265038 Neighboring gene SLIT-ROBO Rho GTPase activating protein 1 Neighboring gene ribosomal protein L36a pseudogene 41

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry. Jae LT, et al. Science, 2013 Apr 26. PMID 23519211, Free PMC Article
  2. Identification of mutations in TMEM5 and ISPD as a cause of severe cobblestone lissencephaly. Vuillaumier-Barrot S, et al. Am J Hum Genet, 2012 Dec 7. PMID 23217329, Free PMC Article
  3. Cell endogenous activities of fukutin and FKRP coexist with the ribitol xylosyltransferase, TMEM5. Nishihara R, et al. Biochem Biophys Res Commun, 2018 Mar 18. PMID 29477842
  4. The Muscular Dystrophy Gene TMEM5 Encodes a Ribitol β1,4-Xylosyltransferase Required for the Functional Glycosylation of Dystroglycan. Manya H, et al. J Biol Chem, 2016 Nov 18. PMID 27733679, Free PMC Article
  5. Direct Mapping of Additional Modifications on Phosphorylated O-glycans of α-Dystroglycan by Mass Spectrometry Analysis in Conjunction with Knocking Out of Causative Genes for Dystroglycanopathy. Yagi H, et al. Mol Cell Proteomics, 2016 Nov. PMID 27601598, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RETINAL MANIFESTATIONS OF WALKER-WARBURG SYNDROME IN TWO SIBLINGS WITH RXYLT1 MUTATIONS.
    Title: RETINAL MANIFESTATIONS OF WALKER-WARBURG SYNDROME IN TWO SIBLINGS WITH RXYLT1 MUTATIONS.
  2. Fukutin, FKRP, and TMEM5 form a complex while maintaining each of their enzyme activities. Data showed that endogenous fukutin and FKRP enzyme activities coexist with TMEM5 enzyme activity, and suggest the possibility that formation of this enzyme complex may contribute to specific and prompt biosynthesis of glycans that are required for dystroglycan function.
    Title: Cell endogenous activities of fukutin and FKRP coexist with the ribitol xylosyltransferase, TMEM5.
  3. TMEM5 is a UDP-xylosyl transferase that elaborates the O-mannose glycan structure on alpha-dystroglycan. The authors demonstrate in a zebrafish model as well as in a human patient that defects in TMEM5 result in muscular dystrophy in combination with abnormal brain development.
    Title: The functional O-mannose glycan on α-dystroglycan contains a phospho-ribitol primed for matriglycan addition.
  4. TMEM5 acts as a UDP-d-xylose:ribitol-5-phosphate beta1,4-xylosyltransferase in the biosynthetic pathway of O-mannosyl glycan.
    Title: The Muscular Dystrophy Gene TMEM5 Encodes a Ribitol β1,4-Xylosyltransferase Required for the Functional Glycosylation of Dystroglycan.
  5. TMEM5 mutations were frequently associated with gonadal dysgenesis and neural tube defects, and ISPD mutations were frequently associated with brain vascular anomalies.
    Title: Identification of mutations in TMEM5 and ISPD as a cause of severe cobblestone lissencephaly.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10
MedGen: C3554381 OMIM: 615041 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribitol beta-1,4-xylosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ribitol beta-1,4-xylosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ribitol beta-1,4-xylosyltransferase activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein O-linked mannosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein O-linked mannosylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein O-linked mannosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
ribitol-5-phosphate xylosyltransferase 1
Names
UDP-D-xylose:ribitol-5-phosphate beta1,4-xylosyltransferase
transmembrane protein 5
type II membrane protein
NP_001265166.1
NP_055069.1
XP_047284034.1
XP_047284035.1
XP_054226740.1
XP_054226741.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033244.1 RefSeqGene

    Range
    5107..34760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278237.2 → NP_001265166.1  ribitol-5-phosphate xylosyltransferase 1 isoform 2

    See identical proteins and their annotated locations for NP_001265166.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC084357, BC013152, BM547839, BX647419
    UniProtKB/Swiss-Prot
    Q9Y2B1
    UniProtKB/TrEMBL
    G3V1K2

  2. NM_014254.3 → NP_055069.1  ribitol-5-phosphate xylosyltransferase 1 isoform 1

    See identical proteins and their annotated locations for NP_055069.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC084357, AI458269, AK289382, BC002596
    Consensus CDS
    CCDS8966.1
    UniProtKB/Swiss-Prot
    A8K017, Q6PKD6, Q9Y2B1
    Related
    ENSP00000261234.6, ENST00000261234.11

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    63779909..63809562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428079.1 → XP_047284035.1  ribitol-5-phosphate xylosyltransferase 1 isoform X2

    UniProtKB/TrEMBL
    A0A8I5KWX9
    Related
    ENSP00000508435.1, ENST00000690060.1

  2. XM_047428078.1 → XP_047284034.1  ribitol-5-phosphate xylosyltransferase 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    63758617..63788268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370766.1 → XP_054226741.1  ribitol-5-phosphate xylosyltransferase 1 isoform X2

    UniProtKB/TrEMBL
    A0A8I5KWX9

  2. XM_054370765.1 → XP_054226740.1  ribitol-5-phosphate xylosyltransferase 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2B1.1 GenPept UniProtKB/Swiss-Prot:Q9Y2B1

Gene LinkOut

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