ALG1 ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: ALG1provided by HGNC
Official Full Name: ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:18294
See related: Ensembl:ENSG00000033011 MIM:605907; AllianceGenome:HGNC:18294
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: HMT1; MT-1; CDG1K; HMAT1; HMT-1; Mat-1; hMat-1
Summary: The enzyme encoded by this gene catalyzes the first mannosylation step in the biosynthesis of lipid-linked oligosaccharides. This gene is mutated in congenital disorder of glycosylation type Ik. [provided by RefSeq, Dec 2008]
Expression: Ubiquitous expression in testis (RPKM 6.0), colon (RPKM 5.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (5071843..5087379)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (5101343..5116882)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (5121844..5137380)

Chromosome 16 - NC_000016.10 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?

evaluated the genetic association of WDR3 and ALG1 in schizophrenia. We examined 21 single nucleotide polymorphisms [SNPs; W1 (rs1812607)-W16 (rs6656360), A1 (rs8053916)-A10 (rs9673733)] from these genes using the Japanese case-control sample (1,808 schizophrenics and 2,170 matched controls). No significant genetic associations of these SNPs were identified. However, we detected a significant association of W4 (rs319471)
Title: Association studies of WD repeat domain 3 and chitobiosyldiphosphodolichol beta-mannosyltransferase genes with schizophrenia in a Japanese population.
Study presents molecular, clinical and biochemical findings in the largest collection of ALG1-CDG cases ever reported at a single time with 39 cases, bringing the total number to 57. This ranks it the third most common CDG type behind PMM2-CDG and ALG6-CDG. In addition, highly lethal genotype were identified and confirm the presence of a unique xeno-tetrasaccharide in ALG1-CDG patients.
Title: ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients.
Was detected in the patient's ALG1-coding sequence.
Title: ALG1-CDG: a new case with early fatal outcome.
Family study defining the phenotype of deficiency of beta-1,4 mannosyltransferase (MT-1) congenital disorder of glycosylation (CDG), due to ALG1 gene mutations. Four novel ALG1 mutations were identified.
Title: Defining the phenotype in congenital disorder of glycosylation due to ALG1 mutations.
DNA sequencing of ALG1 revealed nine different mutations, seven of which have not been previously reported. Clinical presentations of deficiency are severe, with dysmorphias, CNS involvement and ocular disturbances
Title: Guanosine diphosphate-mannose:GlcNAc2-PP-dolichol mannosyltransferase deficiency (congenital disorders of glycosylation type Ik): five new patients and seven 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.

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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
ALG1-congenital disorder of glycosylation MedGen: C2931005 OMIM: 608540 GeneReviews: Congenital Disorders of N-Linked Glycosylation and Multiple Pathway Overview	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. 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

SB153__6903 (e-PCR)
- UniSTS:468673

a06503sbk (e-PCR)
- UniSTS:96247

KS608 (e-PCR)
- UniSTS:253179

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chitobiosyldiphosphodolichol beta-mannosyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables chitobiosyldiphosphodolichol beta-mannosyltransferase activity	TAS Traceable Author Statement more info
enables mannosyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in dolichol-linked oligosaccharide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in dolichol-linked oligosaccharide biosynthetic process	TAS Traceable Author Statement more info
acts_upstream_of_positive_effect protein N-linked glycosylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein glycosylation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasmic side of endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed

General protein information

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Preferred Names: chitobiosyldiphosphodolichol beta-mannosyltransferase

Names: GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase; GDP-mannose-dolichol diphosphochitobiose mannosyltransferase; asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase); asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog; asparagine-linked glycosylation protein 1 homolog; beta-1,4-mannosyltransferase; mannosyltransferase-1; mutant ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase

NP_001317433.1

EC 2.4.1.142

NP_061982.3

EC 2.4.1.142

XP_016878946.1

EC 2.4.1.142

XP_054169468.1

EC 2.4.1.142

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_009202.1 RefSeqGene

Range

5035..20571

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001330504.2 → NP_001317433.1 chitobiosyldiphosphodolichol beta-mannosyltransferase isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate 5' terminal exon, resulting in a distinct 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1

Source sequence(s)

AA810665, AC026458, AK298144, BX370817

Consensus CDS

CCDS81946.1

UniProtKB/TrEMBL

A0A804HJQ1

Related

ENSP00000440019.1, ENST00000544428.1
NM_019109.5 → NP_061982.3 chitobiosyldiphosphodolichol beta-mannosyltransferase isoform 1

See identical proteins and their annotated locations for NP_061982.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC026458

Consensus CDS

CCDS10528.1

UniProtKB/Swiss-Prot

B4DP08, Q6UVZ9, Q8N5Y4, Q9BT22, Q9P2Y2

UniProtKB/TrEMBL

A0A804HKX7

Related

ENSP00000262374.5, ENST00000262374.10

Conserved Domains (2) summary

cd03816
Location:30 → 461

GT1_ALG1_like; This family is most closely related to the GT1 family of glycosyltransferases. The yeast gene ALG1 has been shown to function as a mannosyltransferase that catalyzes the formation of dolichol pyrophosphate (Dol-PP)-GlcNAc2Man from GDP-Man and ...

PLN02275
Location:27 → 424

PLN02275; transferase, transferring glycosyl groups