Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10195
Gene name	ALG3 alpha-1,3- mannosyltransferase
Gene symbol	ALG3
Synonyms (NCBI Gene)	CDG1DCDGS4CDGS6D16Ertd36eNOT56LNot56not
Chromosome	3
Chromosome location	3q27.1
Summary	This gene encodes a member of the ALG3 family. The encoded protein catalyses the addition of the first dol-P-Man derived mannose in an alpha 1,3 linkage to Man5GlcNAc2-PP-Dol. Defects in this gene have been associated with congenital disorder of glycosyla

Show/Hide all (16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs2233466	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs28940588	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103236	C>A,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103237	A>G	Pathogenic	Non coding transcript variant, coding sequence variant, 5 prime UTR variant, intron variant, missense variant
rs119103238	A>G,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs186946267	C>G,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs367679074	C>T	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs370434427	C>A,G,T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs748878963	C>A	Likely-pathogenic	Splice donor variant
rs1028791709	T>C	Likely-pathogenic	Missense variant, 5 prime UTR variant, intron variant, non coding transcript variant, coding sequence variant
rs1085307980	A>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1085307981	T>C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1553827968	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1560162116	T>C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1560164682	T>C	Likely-pathogenic	Intron variant
rs1577105039	T>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

Show/Hide all (25)

miRTarBase ID	miRNA	Experiments	Reference
MIRT005225	hsa-let-7b-5p	pSILAC	18668040
MIRT005258	hsa-miR-16-5p	pSILAC	18668040
MIRT023511	hsa-miR-1-3p	Proteomics	18668040
MIRT025687	hsa-miR-7-5p	Microarray	19073608
MIRT027484	hsa-miR-98-5p	Microarray	19088304
MIRT028778	hsa-miR-26b-5p	Microarray	19088304
MIRT005258	hsa-miR-16-5p	Proteomics;Other	18668040
MIRT005258	hsa-miR-16-5p	Microarray	21199864
MIRT005225	hsa-let-7b-5p	Proteomics;Other	18668040
MIRT048444	hsa-miR-100-5p	CLASH	23622248
MIRT046832	hsa-miR-222-3p	CLASH	23622248
MIRT778540	hsa-miR-1200	CLIP-seq
MIRT778541	hsa-miR-3126-5p	CLIP-seq
MIRT778542	hsa-miR-3132	CLIP-seq
MIRT778543	hsa-miR-3153	CLIP-seq
MIRT778544	hsa-miR-3529	CLIP-seq
MIRT778545	hsa-miR-379	CLIP-seq
MIRT778546	hsa-miR-3936	CLIP-seq
MIRT778547	hsa-miR-4324	CLIP-seq
MIRT778548	hsa-miR-4419a	CLIP-seq
MIRT778549	hsa-miR-4436b-3p	CLIP-seq
MIRT778550	hsa-miR-4510	CLIP-seq
MIRT778551	hsa-miR-4726-3p	CLIP-seq
MIRT778552	hsa-miR-510	CLIP-seq
MIRT778553	hsa-miR-544b	CLIP-seq

Show/Hide all (20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000030	Function	Mannosyltransferase activity	IEA
GO:0000033	Function	Alpha-1,3-mannosyltransferase activity	TAS
GO:0005515	Function	Protein binding	IPI	21516116, 25910212, 29547901, 31515488, 32296183
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	10581255
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006486	Process	Protein glycosylation	IBA
GO:0006486	Process	Protein glycosylation	IEA
GO:0006487	Process	Protein N-linked glycosylation	IDA	10581255
GO:0006488	Process	Dolichol-linked oligosaccharide biosynthetic process	IDA	10581255
GO:0006488	Process	Dolichol-linked oligosaccharide biosynthetic process	TAS
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0052925	Function	Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity	IBA
GO:0052925	Function	Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity	IDA	10581255
GO:0052925	Function	Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity	IEA
GO:0098553	Component	Lumenal side of endoplasmic reticulum membrane	IC	10581255

MIM	HGNC	e!Ensembl
608750	23056	ENSG00000214160

Q92685

Protein name

Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase (EC 2.4.1.258) (Asparagine-linked glycosylation protein 3 homolog) (Dol-P-Man-dependent alpha(1-3)-mannosyltransferase) (Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase) (Dolich

Protein function

Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation. The assembly of dolichol-linked

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05208	ALG3	47 → 406	ALG3 protein	Family

Sequence

MAAGLRKRGRSGSAAQAEGLCKQWLQRAWQERRLLLREPRYTLLVAACLCLAEVGITFWV
IHRVAYTEIDWKAYMAEVEGVINGTYDYTQLQGDTGPLVYPAGFVYIFMGLYYATSRGTD
IRMAQNIFAVLYLATLLLVFLIYHQTCKVPPFVFFFMCCASYRVHSIFVLRLFNDPVAMV
LLFLSINLLLAQRWGWGCCFFSLAVSVKMNVLLFAPGLLFLLLTQFGFRGALPKLGICAG
LQVVLGLPFLLENPSGYLSRSFDLGRQFLFHWTVNWRFLPEALFLHRAFHLALLTAHLTL
LLLFALCRWHRTGESILSLLRDPSKRKVPPQPLTPNQIVSTLFTSNFIGICFSRSLHYQF
YVWYFHTLPYLLWAMPARWLTHLLRLLVLGLIELSWNTYPSTSCSSAALHICHAVILLQL
WLGPQPFPKSTQHSKKAH

Sequence length

438

Interactions

View interactions

	KEGG		Reactome
	N-Glycan biosynthesis Various types of N-glycan biosynthesis Metabolic pathways		Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein Defective ALG3 causes ALG3-CDG (CDG-1d)

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
ALG3-congenital disorder of glycosylation	Pathogenic; Likely pathogenic	rs546890576, rs1023520147, rs376927697, rs747953768, rs1719068613, rs2108442073, rs28940588, rs387906273, rs119103236, rs119103238, rs2473846363, rs762510540, rs2473859485, rs1287098925, rs770044637 View all (10 more)	RCV001361335 RCV001526666 RCV001543410 RCV001543406 RCV001543411 View all (20 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Congenital disorder of glycosylation	Likely pathogenic	rs1718972826	RCV004018348	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (25)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALG3-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION TYPE 1D	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE ID	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Lung cancer	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (42)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
ALG3-CDG	Congenital Disorder Of Glycosylation	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthrogryposis	Arthrogryposis multiplex congenita	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29799832		★★★★★ ★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type 1s	Congenital disorder of glycosylation	BEFREE	26126960, 31067009		★★★★★ ★☆☆☆☆ Found in Text Mining only
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id	Congenital disorder of glycosylation	UNIPROT_DG	10581255, 15840742		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id	Congenital disorder of glycosylation	BEFREE	15108280, 16053906, 16079417, 18679822, 23791010		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	16006436, 19862844, 27604308		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id	Congenital disorder of glycosylation	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id	Congenital disorder of glycosylation	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE If	Congenital disorder of glycosylation	BEFREE	16079417		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	23791010, 26126960, 28122681, 28742265, 29547901, 31067009		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	26805780, 32389449, 32655146, 34440401, 35211808	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	32389449	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Familial Alzheimer Disease (FAD)	Alzheimer disease	BEFREE	8940094, 9106304		★★★★★ ★☆☆☆☆ Found in Text Mining only
Food intolerance (disorder)	Food Intolerance	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Laryngeal Squamous Cell Carcinoma	Laryngeal Carcinoma	BEFREE	30805892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	29880818		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	31899049	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29799832		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	29547901, 30805892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 9	Nail Diseases	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nail dysplasia	Nail dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	40083705	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29799832, 30805892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	24203761		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	30805892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	40312703	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	17504382	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

ALG3 (ALG3 alpha-1,3- mannosyltransferase)