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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	29925
Gene name Gene Name - the full gene name approved by the HGNC.	GDP-mannose pyrophosphorylase B
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	GMPPB
Synonyms (NCBI Gene) Gene synonyms aliases	LGMDR19, MDDGA14, MDDGB14, MDDGC14
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p21.31
Summary Summary of gene provided in NCBI Entrez Gene.	This gene is thought to encode a GDP-mannose pyrophosphorylase. The encoded protein catalyzes the conversion of mannose-1-phosphate and GTP to GDP-mannose, a reaction involved in the production of N-linked oligosaccharides. Alternatively spliced transcrip

Show/Hide all(21)

SNP ID	Visualize variation	Clinical significance	Consequence
rs141588721	C>G,T	Likely-pathogenic	Splice donor variant
rs142336618	C>G	Pathogenic	Missense variant, coding sequence variant
rs142908436	G>A,T	Pathogenic, likely-pathogenic	Missense variant, synonymous variant, coding sequence variant
rs145564018	C>T	Likely-pathogenic	Splice donor variant
rs202013297	G>A	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs202160208	C>T	Pathogenic	Coding sequence variant, missense variant
rs397509423	G>A	Pathogenic	Coding sequence variant, stop gained
rs397509424	G>A	Pathogenic	Missense variant, coding sequence variant
rs397509425	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs397509426	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs761714818	A>G	Pathogenic	Missense variant, coding sequence variant
rs763971677	G>A	Pathogenic	Coding sequence variant, stop gained
rs875989850	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs875989851	G>A	Pathogenic	Missense variant, coding sequence variant
rs886039382	C>T	Pathogenic	Splice acceptor variant
rs1191822017	CGGGCCAGCGCCA>-	Pathogenic	Frameshift variant, coding sequence variant
rs1348189028	G>A	Pathogenic	Stop gained, coding sequence variant
rs1553691918	GT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553691975	->CT	Pathogenic	Frameshift variant, coding sequence variant
rs1559697183	G>A	Pathogenic	Stop gained, coding sequence variant
rs1559697515	T>C	Likely-pathogenic	Missense variant, coding sequence variant

Show/Hide all(26)

miRTarBase ID	miRNA	Experiments	Reference
MIRT019376	hsa-miR-148b-3p	Microarray	17612493
MIRT043742	hsa-miR-328-3p	CLASH	23622248
MIRT041226	hsa-miR-193b-3p	CLASH	23622248
MIRT1022740	hsa-miR-214	CLIP-seq
MIRT1022741	hsa-miR-3151	CLIP-seq
MIRT1022742	hsa-miR-3170	CLIP-seq
MIRT1022743	hsa-miR-342-5p	CLIP-seq
MIRT1022744	hsa-miR-3619-5p	CLIP-seq
MIRT1022745	hsa-miR-4265	CLIP-seq
MIRT1022746	hsa-miR-4296	CLIP-seq
MIRT1022747	hsa-miR-4322	CLIP-seq
MIRT1022748	hsa-miR-4447	CLIP-seq
MIRT1022749	hsa-miR-4455	CLIP-seq
MIRT1022750	hsa-miR-4472	CLIP-seq
MIRT1022751	hsa-miR-4481	CLIP-seq
MIRT1022752	hsa-miR-4530	CLIP-seq
MIRT1022753	hsa-miR-4651	CLIP-seq
MIRT1022754	hsa-miR-4664-5p	CLIP-seq
MIRT1022755	hsa-miR-4713-3p	CLIP-seq
MIRT1022756	hsa-miR-4722-3p	CLIP-seq
MIRT1022757	hsa-miR-4745-5p	CLIP-seq
MIRT1022758	hsa-miR-491-5p	CLIP-seq
MIRT1022759	hsa-miR-608	CLIP-seq
MIRT1022760	hsa-miR-761	CLIP-seq
MIRT2003163	hsa-miR-361-3p	CLIP-seq
MIRT2003164	hsa-miR-4313	CLIP-seq

Show/Hide all(23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004475	Function	Mannose-1-phosphate guanylyltransferase (GTP) activity	EXP	33986552
GO:0004475	Function	Mannose-1-phosphate guanylyltransferase (GTP) activity	IBA
GO:0004475	Function	Mannose-1-phosphate guanylyltransferase (GTP) activity	IDA	33986552
GO:0004475	Function	Mannose-1-phosphate guanylyltransferase (GTP) activity	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 25416956, 31515488, 32296183, 33961781, 33986552
GO:0005525	Function	GTP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	23768512
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006486	Process	Protein glycosylation	IBA
GO:0009298	Process	GDP-mannose biosynthetic process	IBA
GO:0009298	Process	GDP-mannose biosynthetic process	IEA
GO:0009298	Process	GDP-mannose biosynthetic process	IMP	26310427
GO:0009298	Process	GDP-mannose biosynthetic process	TAS
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0019673	Process	GDP-mannose metabolic process	IDA	33986552
GO:0046872	Function	Metal ion binding	IEA
GO:0061728	Process	GDP-mannose biosynthetic process from mannose	IEA
GO:0120508	Component	GDP-mannose pyrophosphorylase complex	IDA	33986552

MIM	HGNC	e!Ensembl
615320	22932	ENSG00000173540

Protein

UniProt ID

Q9Y5P6

Protein name

Mannose-1-phosphate guanylyltransferase catalytic subunit beta (EC 2.7.7.13) (GDP-mannose pyrophosphorylase B) (GTP-mannose-1-phosphate guanylyltransferase beta)

Protein function

Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate guanylyltransferase complex (PubMed:33986552). Catalyzes the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids (PubMed:33986552). Can cat

PDB

7D72 , 7D73 , 7D74

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00483	NTP_transferase	2 → 235	Nucleotidyl transferase	Family
PF00132	Hexapep	259 → 294	Bacterial transferase hexapeptide (six repeats)	Repeat

Tissue specificity

TISSUE SPECIFICITY: [Isoform 1]: Ubiquitously expressed, including in brain and skeletal muscle. {ECO:0000269|PubMed:23768512}.; TISSUE SPECIFICITY: [Isoform 2]: Weakly expressed with highest expression in skeletal muscle, brain and gonads. {ECO:0000269|P

Sequence

MKALILVGGYGTRLRPLTLSTPKPLVDFCNKPILLHQVEALAAAGVDHVILAVSYMSQVL
EKEMKAQEQRLGIRISMSHEEEPLGTAGPLALARDLLSETADPFFVLNSDVICDFPFQAM
VQFHRHHGQEGSILVTKVEEPSKYGVVVCEADTGRIHRFVEKPQVFVSNKINAGMYILSP
AVLQRIQLQPTSIEKEVFPIMAKEGQLYAMELQGFWMDIGQPKDFLTGMCLFLQSLRQKQ
PERLCSGPGIVGNVLVDPSARIGQNCSIGPNVSLGPGVVVEDGVCIRRCTVLRDARIRSH
SWLESCIVGWRCRVGQWVRMENVTVLGEDVIVNDELYLNGASVLPHKSIGESVPEPRIIM

Sequence length

360

Interactions

View interactions

	KEGG
	Fructose and mannose metabolism Amino sugar and nucleotide sugar metabolism Metabolic pathways Biosynthesis of cofactors Biosynthesis of nucleotide sugars

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Muscular dystrophy	muscular dystrophy	rs142908436	N/A
Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14	rs397509423, rs141588721, rs202160208, rs397509422	N/A
Limb-girdle muscular dystrophy	Autosomal recessive limb-girdle muscular dystrophy type 2T	rs875989850, rs397509424, rs875989851, rs397509425, rs397509426, rs1559697515, rs202160208, rs142336618, rs199922550, rs397509422, rs142908436	N/A
muscular dystrophy-dystroglycanopathy	Muscular dystrophy-dystroglycanopathy	rs199922550	N/A

Show/Hide Unknown Diseases (7)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Congenital Muscular Dystrophy With Cerebellar Involvement	congenital muscular dystrophy with cerebellar involvement	N/A	N/A	GenCC
Congenital Muscular Dystrophy With Intellectual Disability	congenital muscular dystrophy with intellectual disability	N/A	N/A	GenCC
Congenital Myasthenic Syndromes With Glycosylation Defect	congenital myasthenic syndromes with glycosylation defect	N/A	N/A	GenCC
Developmental Delay	global developmental delay	N/A	N/A	ClinVar
Muscle Eye Brain Disease	muscle-eye-brain disease	N/A	N/A	GenCC
Myasthenic Syndrome	congenital myasthenic syndrome	N/A	N/A	GenCC
Myopathy	myopathy caused by variation in GMPPB	N/A	N/A	GenCC

Show/Hide Text Mining Associations (18)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenomyosis	Associate	40527793
Arthrogryposis	Associate	33060286
Autism Spectrum Disorder	Associate	30257713
Congenital Disorders of Glycosylation	Associate	35211808
Epilepsy	Associate	26310427
Epilepsy Generalized	Associate	24780531
Fabry Disease	Associate	30257713
Facioscapulohumeral muscular dystrophy 1a	Associate	33386810
Glioblastoma	Associate	37834154
Hereditary Myopathy with Early Respiratory Failure	Associate	34633329
Muscular Diseases	Associate	26133662, 30257713, 35723113
Muscular Dystrophies	Associate	24780531, 25353622, 26133662, 26310427, 31378432
Muscular Dystrophies Limb Girdle	Associate	24035193, 26310427, 26404900, 31211170, 33386810, 34633329
Myasthenic Syndromes Congenital	Associate	26133662, 27147698, 30257713, 31211170, 31378432, 34633329, 35670010, 36308527, 37721175
Myopathies Structural Congenital	Associate	31378432
Neuromuscular Junction Diseases	Associate	26133662, 31378432, 32115343
Retinal Dystrophies	Associate	34633329
Walker Warburg Syndrome	Associate	24780531, 26133662, 26310427, 30060766, 30257713, 31211170, 32115343, 34633329

GMPPB (GDP-mannose pyrophosphorylase B)