RXYLT1 ribitol xylosyltransferase 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.

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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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH77947 (e-PCR)
- UniSTS:47672

RH80375 (e-PCR)
- UniSTS:90689

RH98695 (e-PCR)
- UniSTS:88163

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

EC 2.4.2.61

NP_055069.1

EC 2.4.2.61

XP_047284034.1

EC 2.4.2.61

XP_047284035.1

EC 2.4.2.61

XP_054226740.1

EC 2.4.2.61

XP_054226741.1

EC 2.4.2.61

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

NG_033244.1 RefSeqGene

Range

5107..34760

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

63779909..63809562

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I5KWX9

Related

ENSP00000508435.1, ENST00000690060.1
XM_047428078.1 → XP_047284034.1 ribitol-5-phosphate xylosyltransferase 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

63758617..63788268

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I5KWX9
XM_054370765.1 → XP_054226740.1 ribitol-5-phosphate xylosyltransferase 1 isoform X1