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	29925
Gene name	GDP-mannose pyrophosphorylase B
Gene symbol	GMPPB
Synonyms (NCBI Gene)	LGMDR19MDDGA14MDDGB14MDDGC14
Chromosome	3
Chromosome location	3p21.31
Summary	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

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

969

Show/Hide Causal Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the musculature	Likely pathogenic; Pathogenic	rs2108211362, rs875989851, rs1553691918, rs761714818, rs397509422, rs202160208	RCV001814435 RCV001814120 RCV001814186 RCV001814219 RCV001836725 RCV001814035
Acute rhabdomyolysis	Likely pathogenic; Pathogenic	rs142336618	RCV005865226
Autosomal recessive limb-girdle muscular dystrophy type 2T	Likely pathogenic; Pathogenic	rs2080423660, rs1365085828, rs766298888, rs2108213393, rs764625823, rs1210040661, rs2080421905, rs769459081, rs2544756965, rs1204528532, rs1283105162, rs2544752296, rs142908436, rs875989850, rs875989851 View all (24 more)	RCV001377618 RCV001384680 RCV001729998 RCV003152771 RCV001991893 RCV002016193 RCV003079049 RCV002667891 RCV002811019 RCV002856752 RCV002971529 RCV003043757 RCV000211126 RCV000211128 RCV000211125 RCV003152978 RCV003796722 RCV003810383 RCV000527021 RCV000551670 RCV003104002 RCV000690678 RCV000698360 RCV000692931 RCV000690893 RCV005213382 RCV000815814 RCV000821842 RCV000801856 RCV000794094 RCV000054433 RCV000054435 RCV000054437 RCV000209926 RCV000209893 RCV000054440 RCV000054441 RCV001197852 RCV001241608
Elevated circulating creatine kinase concentration	Pathogenic	rs1559697515	RCV000678462
GMPPB-related disorder	Likely pathogenic; Pathogenic	rs761714818, rs202013297, rs141588721, rs397509422, rs202160208, rs142336618	RCV004547864 RCV005870880 RCV004782552 RCV004549480 RCV003407434 RCV003421962
Limb-girdle muscular dystrophy	Likely pathogenic; Pathogenic	rs397509422	RCV005625254
Muscular dystrophy	Pathogenic; Likely pathogenic	rs142908436, rs142336618	RCV000609930 RCV000610921
Muscular dystrophy-dystroglycanopathy	Likely pathogenic; Pathogenic	rs397509425, rs199922550	RCV000503216 RCV000501778
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14	Likely pathogenic; Pathogenic	rs2080423660, rs1365085828, rs764625823, rs1210040661, rs2080421905, rs769459081, rs2544756965, rs1204528532, rs1283105162, rs2544752296, rs142908436, rs875989850, rs2080456894, rs2544753930, rs141588721 View all (18 more)	RCV001377618 RCV001384680 RCV001991893 RCV002016193 RCV003079049 RCV002667891 RCV002811019 RCV002856752 RCV002971529 RCV003043757 RCV000698947 RCV002515608 RCV003796722 RCV003810383 RCV004820857 RCV000527021 RCV000551670 RCV000690678 RCV000698360 RCV000692931 RCV000690893 RCV005213382 RCV000815814 RCV000821842 RCV000801856 RCV000794094 RCV000054432 RCV000054434 RCV000200261 RCV000684892 RCV000553832 RCV000533184 RCV000651278 RCV001241608
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14	Likely pathogenic; Pathogenic	rs2080423660, rs1365085828, rs764625823, rs1210040661, rs2080421905, rs769459081, rs2544756965, rs1204528532, rs1283105162, rs2544752296, rs142908436, rs875989850, rs2080456894, rs2544753930, rs1553691975 View all (17 more)	RCV001377618 RCV001384680 RCV001991893 RCV002016193 RCV003079049 RCV002667891 RCV002811019 RCV002856752 RCV002971529 RCV003043757 RCV000698947 RCV002515608 RCV003796722 RCV003810383 RCV000527021 RCV000551670 RCV000690678 RCV000698360 RCV000692931 RCV000690893 RCV005213382 RCV000815814 RCV000821842 RCV000801856 RCV000794094 RCV000651273 RCV000054436 RCV000054438 RCV000054439 RCV000533184 RCV000651278 RCV001241608
Myopathy caused by variation in GMPPB	Likely pathogenic	rs1175885498	RCV003226078

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs886039910	-
Global developmental delay	Uncertain significance	rs1060499721	RCV000449525
Malignant lymphoma, large B-cell, diffuse	Likely benign	rs539632278	RCV005912863
Malignant tumor of esophagus	Likely benign	rs539632278	RCV005912862
Nonpapillary renal cell carcinoma	Likely benign	rs1426684077	RCV005909060
Sarcoma	Uncertain significance	rs746420101	RCV005925537

Show/Hide Text Mining Associations (18)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)