RFT1 RFT1 homolog [Homo sapiens (human)] - Gene

Summary

Official Symbol: RFT1provided by HGNC
Official Full Name: RFT1 homologprovided by HGNC
Primary source: HGNC:HGNC:30220
See related: Ensembl:ENSG00000163933 MIM:611908; AllianceGenome:HGNC:30220
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: CDG1N
Summary: This gene encodes an enzyme which catalyzes the translocation of the Man(5)GlcNAc (2)-PP-Dol intermediate from the cytoplasmic to the luminal side of the endoplasmic reticulum membrane in the pathway for the N-glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type In.[provided by RefSeq, Dec 2008]
Expression: Ubiquitous expression in thyroid (RPKM 1.9), testis (RPKM 1.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.1

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (53066853..53130435, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (53099771..53163318, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (53122499..53164451, complement)

Chromosome 3 - NC_000003.12 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 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?

Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG.
Title: Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG.
A novel RFT1 missense mutation was identified in a family with history of neonatal deaths due to severe respiratory insufficiency.
Title: A family with floppy neonates with severe respiratory insufficiency: A lethal phenotype of RFT1-CDG due to a novel mutation.
showed that this patient was compound heterozygous for two mutations in the RFT1 gene: c.1325G>A (p.R442Q) and c.110G>T (p.R37L)
Title: RFT1-congenital disorder of glycosylation (CDG) syndrome: a cause of early-onset severe epilepsy.
Six patients with RFT1-CDG show sensorineural deafness as part of a severe neurological syndrome
Title: RFT1-CDG: deafness as a novel feature of congenital disorders of glycosylation.
Identification of novel missense mutations in exon 12 of the RFT1 gene in adult siblings with congenital disorder of glycosylation (CDG) syndrome caused by RFT1 deficiency.
Title: RFT1-CDG in adult siblings with novel mutations.
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.
RFT1 deficiency in both yeast and human cells leads to the accumulation of incomplete DolPP-GlcNAc(2)Man(5) and to a profound glycosylation disorder in humans.
Title: Human RFT1 deficiency leads to a disorder of N-linked glycosylation.

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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
RFT1-congenital disorder of glycosylation MedGen: C2677590 OMIM: 612015 GeneReviews: Congenital Disorders of N-Linked Glycosylation and Multiple Pathway Overview	not available

EBI GWAS Catalog

Description
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 13 new risk loci for schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D11S2921 (e-PCR)
- UniSTS:152074

GDB:434012 (e-PCR)
- UniSTS:157204

D8S2279 (e-PCR)
- UniSTS:473907

G38154 (e-PCR)
- UniSTS:53341

D10S16 (e-PCR)
- UniSTS:155756

NoName (e-PCR)
- UniSTS:487290

G69469 (e-PCR)
- UniSTS:229515

GDB:182516 (e-PCR)
- UniSTS:155384

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glycolipid floppase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in dolichol-linked oligosaccharide biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glycolipid translocation	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycolipid translocation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein N-linked glycosylation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endoplasmic reticulum membrane	IGI Inferred from Genetic Interaction more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1

Names: RFT1, requiring fifty three 1 homolog; congenital disorder of glycosylation 1N; protein RFT1 homolog; putative endoplasmic reticulum multispan transmembrane protein

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_009203.1 RefSeqGene

Range

5020..46972

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_052859.4 → NP_443091.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1

See identical proteins and their annotated locations for NP_443091.1

Status: REVIEWED

Source sequence(s)

AC096887, AL713685, BC043595

Consensus CDS

CCDS2869.1

UniProtKB/Swiss-Prot

Q96AA3, Q96J03

UniProtKB/TrEMBL

A0A291FGD9

Related

ENSP00000296292.3, ENST00000296292.8

Conserved Domains (1) summary

pfam04506
Location:14 → 524

Rft-1; Rft protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

53066853..53130435 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011534215.4 → XP_011532517.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X2

Related

ENSP00000520849.1, ENST00000850556.1

Conserved Domains (1) summary

cl09326
Location:11 → 403

MATE_like; Multidrug and toxic compound extrusion family and similar proteins
XM_011534214.3 → XP_011532516.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X1

Conserved Domains (1) summary

cl09326
Location:11 → 403

MATE_like; Multidrug and toxic compound extrusion family and similar proteins
XM_006713384.4 → XP_006713447.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X3

Conserved Domains (1) summary

cl09326
Location:11 → 403

MATE_like; Multidrug and toxic compound extrusion family and similar proteins
XM_011534216.4 → XP_011532518.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X5

Conserved Domains (1) summary

cl09326
Location:22 → 305

MATE_like; Multidrug and toxic compound extrusion family and similar proteins
XM_005265537.5 → XP_005265594.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X4

Conserved Domains (1) summary

cl09326
Location:11 → 368

MATE_like; Multidrug and toxic compound extrusion family and similar proteins

RNA

XR_007095765.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

53099771..53163318 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348362.1 → XP_054204337.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X2
XM_054348361.1 → XP_054204336.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X1
XM_054348363.1 → XP_054204338.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X3
XM_054348365.1 → XP_054204340.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X5
XM_054348364.1 → XP_054204339.1 man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X4