PGM1 (phosphoglucomutase 1)

Gene

• Entrez ID: 5236
• Gene name: Phosphoglucomutase 1
• Gene symbol: PGM1
• Synonyms (NCBI Gene): CDG1T, GSD14
• Chromosome: 1
• Chromosome location: 1p31.3
• Summary: The protein encoded by this gene is an isozyme of phosphoglucomutase (PGM) and belongs to the phosphohexose mutase family. There are several PGM isozymes, which are encoded by different genes and catalyze the transfer of phosphate between the 1 and 6 posi

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918371	A>C,G	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant
rs397515423	C>T	Pathogenic	Coding sequence variant, stop gained
rs398122912	G>A,C,T	Pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs587776801	G>C	Pathogenic	Splice acceptor variant
rs587777401	T>C,G	Pathogenic	Coding sequence variant, missense variant
rs587777402	A>T	Pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant, upstream transcript variant
rs587777403	G>C	Pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant, upstream transcript variant
rs587777404	G>T	Pathogenic	Coding sequence variant, missense variant
rs587777405	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs763428801	TC>-	Pathogenic	Frameshift variant, coding sequence variant
rs770066171	C>T	Pathogenic	Stop gained, coding sequence variant
rs1170935238	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1302961946	T>A,C	Likely-pathogenic	Synonymous variant, coding sequence variant, stop gained
rs1557437034	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1557445467	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1570463842	CC>-	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant, upstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT005175	hsa-miR-30a-5p	pSILAC	18668040
MIRT002597	hsa-miR-124-3p	Microarray	15685193
MIRT002597	hsa-miR-124-3p	Microarray	18668037
MIRT002597	hsa-miR-124-3p	Microarray	15685193
MIRT005175	hsa-miR-30a-5p	Proteomics;Other	18668040
MIRT052231	hsa-let-7b-5p	CLASH	23622248
MIRT1227548	hsa-miR-124	CLIP-seq
MIRT1227549	hsa-miR-3125	CLIP-seq
MIRT1227550	hsa-miR-3133	CLIP-seq
MIRT1227551	hsa-miR-3147	CLIP-seq
MIRT1227552	hsa-miR-33a	CLIP-seq
MIRT1227553	hsa-miR-33b	CLIP-seq
MIRT1227554	hsa-miR-3916	CLIP-seq
MIRT1227555	hsa-miR-3940-5p	CLIP-seq
MIRT1227556	hsa-miR-4257	CLIP-seq
MIRT1227557	hsa-miR-4425	CLIP-seq
MIRT1227558	hsa-miR-4507	CLIP-seq
MIRT1227559	hsa-miR-4511	CLIP-seq
MIRT1227560	hsa-miR-4520a-3p	CLIP-seq
MIRT1227561	hsa-miR-4520b-3p	CLIP-seq
MIRT1227562	hsa-miR-4666-5p	CLIP-seq
MIRT1227563	hsa-miR-506	CLIP-seq
MIRT1227564	hsa-miR-509-3p	CLIP-seq
MIRT1227564	hsa-miR-509-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000287	Function	Magnesium ion binding	IDA	26972339
GO:0000287	Function	Magnesium ion binding	IEA
GO:0004614	Function	Phosphoglucomutase activity	IBA
GO:0004614	Function	Phosphoglucomutase activity	IDA	1530890, 25288802, 30982613
GO:0004614	Function	Phosphoglucomutase activity	IEA
GO:0004614	Function	Phosphoglucomutase activity	TAS	8257433
GO:0005515	Function	Protein binding	IPI	21044950
GO:0005576	Component	Extracellular region	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	1530890
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	TAS
GO:0005975	Process	Carbohydrate metabolic process	IBA
GO:0005975	Process	Carbohydrate metabolic process	IEA
GO:0006006	Process	Glucose metabolic process	IDA	25288802
GO:0006006	Process	Glucose metabolic process	IEA
GO:0006006	Process	Glucose metabolic process	IEA
GO:0006006	Process	Glucose metabolic process	NAS	1530890
GO:0006094	Process	Gluconeogenesis	TAS	8257433
GO:0006096	Process	Glycolytic process	TAS	8257433
GO:0016853	Function	Isomerase activity	IEA
GO:0016868	Function	Intramolecular phosphotransferase activity	IEA
GO:0033499	Process	Galactose catabolic process via UDP-galactose, Leloir pathway	IMP	30982613
GO:0046872	Function	Metal ion binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:1904724	Component	Tertiary granule lumen	TAS
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

Other IDs

• MIM: 171900
• HGNC: 8905
• e!Ensembl: ENSG00000079739

Protein

• UniProt ID: P36871
• Protein name: Phosphoglucomutase-1 (PGM 1) (EC 5.4.2.2) (Glucose phosphomutase 1)
• Protein function: Catalyzes the reversible isomerization of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate (PubMed:15378030, PubMed:25288802). The mechanism proceeds via the intermediate compound alpha-D-glucose 1,6-bisphosphate (Probable) (PubMed:252
• PDB: 5EPC, 5F9C, 5HSH, 5JN5, 5TR2, 5VBI, 5VEC, 5VG7, 5VIN, 6SNO, 6SNP, 6SNQ, 6UIQ, 6UO6, 7S0W, 7S77
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02878	PGM_PMM_I	14 → 158	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I	Domain
  PF02879	PGM_PMM_II	193 → 301	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II	Domain
  PF02880	PGM_PMM_III	306 → 420	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III	Domain
  PF00408	PGM_PMM_IV	434 → 539	Phosphoglucomutase/phosphomannomutase, C-terminal domain	Family

• Sequence:

  MVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVG
  GDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNP
  GGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENK
  FKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEE
  LGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKH
  GFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASATKIALYETPTGWK
  FFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWQKY
  GRNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPV
  DGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIRLYIDSYEKDVAKINQDPQVMLAPLI
  SIALKVSQLQERTGRTAPTVIT

• Sequence length: 562

Pathways

KEGG:

Glycolysis / Gluconeogenesis
Pentose phosphate pathway
Galactose metabolism
Purine metabolism
Starch and sucrose metabolism
Amino sugar and nucleotide sugar metabolism
Metabolic pathways
Biosynthesis of nucleotide sugars

Reactome:

Glycogen synthesis
Defective PGM1 causes PGM1-CDG (CDG1t)
Neutrophil degranulation

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Congenital disorder of glycosylation	Likely pathogenic; Pathogenic	rs1453920894	RCV004798932	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PGM1-congenital disorder of glycosylation	Likely pathogenic; Pathogenic	rs777164338, rs1649810314, rs2100982320, rs587777401, rs587777402, rs587777404, rs587777405, rs1376645472, rs2100988650, rs1453920894, rs759220275, rs2523892264, rs2523892321, rs377295149, rs2523788919, rs772768778, rs1649153115, rs752562811, rs2523892266, rs2523941865, rs121918371, rs587776801, rs2523895823, rs398122912, rs397515423, rs770066171, rs1557437034, rs1570463842, rs1170935238, rs763428801, rs1647935062, rs745993071	RCV001378469 RCV001377288 RCV001733873 RCV000119799 RCV000119800 RCV000119802 RCV000119803 RCV001953214 RCV001895588 RCV001904562 RCV003653592 RCV002466307 RCV002466308 RCV003065371 RCV003079003 RCV002648157 RCV002856493 RCV003331588 RCV003487101 RCV003536106 RCV000014620 RCV000014621 RCV003649573 RCV000032990 RCV000032991 RCV000596556 RCV000703389 RCV000820907 RCV000810297 RCV000799107 RCV001239446 RCV001253738	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PGM1-related disorder	Likely pathogenic; Pathogenic	rs777164338, rs587777404, rs772768778	RCV004734161 RCV004529993 RCV004538859	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IT	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCOGEN STORAGE DISEASE XIV	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL ISCHEMIA	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 1 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	24558171	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis, Psoriatic	Psoriatic Arthritis	BEFREE	3157636		★☆☆☆☆ Found in Text Mining only
Brain Diseases Metabolic Inborn	Brain disease	Pubtator	25288802	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	BEFREE	30262252, 31563034		★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Dilated	Dilated cardiomyopathy	Pubtator	25288802	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Familial Idiopathic	Cardiomyopathy	BEFREE	19377068		★☆☆☆☆ Found in Text Mining only
Charcot-Marie-Tooth Disease	Charcot-Marie-Tooth Disease	BEFREE	6952764		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	CTD_human_DG	25944804		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	CTD_human_DG	25944804		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complete hydatidiform mole	Complete Hydatidiform Mole	BEFREE	2821529		★☆☆☆☆ Found in Text Mining only
Congenital Disorder Of Glycosylation Type In	Congenital disorder of glycosylation	Pubtator	36214454	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	26972339, 30122451, 33342467, 35506765, 36579437	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	29112118, 29702557, 29858906, 30048639, 30641270, 30737079, 30982613, 31077402, 31563034		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Hyperinsulinism	Hyperinsulinemic hypoglycemia	BEFREE	26908106, 31119523		★☆☆☆☆ Found in Text Mining only
Dermatologic disorders	Dermatologic Disorders	BEFREE	885537		★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	7909309, 8088756, 8743992		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	7909309, 8088756, 8743992		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	19761607	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	GWASDB_DG	19430480		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	GWASCAT_DG	19430480		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	8088756		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	8088756		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	31563034		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	508567	Associate	★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen storage disease	Pubtator	22899091, 24499211, 26972339, 30122451	Associate	★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen Storage Disease	BEFREE	22976764, 28190645, 30048639		★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen Storage Disease	GENOMICS_ENGLAND_DG	27206562, 27604308		★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type V	Glycogen Storage Disease	BEFREE	28882528		★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease XIV	Glycogen Storage Disease	ORPHANET_DG	19625727, 22492991, 24499211		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease XIV	Glycogen Storage Disease	UNIPROT_DG	19625727, 22492991, 22976764, 24499211, 25288802, 26972339		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease XIV	Glycogen Storage Disease	GENOMICS_ENGLAND_DG	19625727, 22492991, 27206562, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease XIV	Glycogen storage disease	Pubtator	24499211, 26972339, 30122451	Inhibit	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease XIV	Glycogen storage disease	Pubtator	25288802, 26972339, 28117557	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease XIV	Glycogen Storage Disease	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease XIV	Glycogen Storage Disease	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperinsulinemic hypoglycemia	Hyperinsulinemic hypoglycemia	BEFREE	29280746		★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	BEFREE	26768186, 30262252		★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	Pubtator	36579437	Associate	★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid	Myeloid leukemia	Pubtator	7684194	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	7684194	Stimulate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	30335765		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	3157636		★☆☆☆☆ Found in Text Mining only
Lupus Nephritis	Lupus Nephritis	LHGDN	18495743		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30335765		★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	BEFREE	25168163, 25288802		★☆☆☆☆ Found in Text Mining only
Miscarriage	Miscarriage	BEFREE	11466970		★☆☆☆☆ Found in Text Mining only
Mood Disorders	Mood Disorder	BEFREE	618816		★☆☆☆☆ Found in Text Mining only
Muscular Atrophy Spinal	Spinal muscular atrophy	Pubtator	2570155	Associate	★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy Facioscapulohumeral	Facioscapulohumeral muscular dystrophy	Pubtator	2570155	Associate	★☆☆☆☆ Found in Text Mining only
Myocardial Ischemia	Myocardial Ischemia	CTD_human_DG	16214533		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Myopathy	Myopathy	BEFREE	30262252		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30335765		★☆☆☆☆ Found in Text Mining only
NGLY1 deficiency	NGLY1 Deficiency	GENOMICS_ENGLAND_DG	27206562, 27604308		★☆☆☆☆ Found in Text Mining only
Papillary thyroid carcinoma	Papillary thyroid carcinoma	BEFREE	31645594		★☆☆☆☆ Found in Text Mining only
PGM1-CDG	Congenital Disorder Of Glycosylation	Orphanet			★☆☆☆☆ Found in Text Mining only
Phenylketonurias	Phenylketonuria	BEFREE	293128		★☆☆☆☆ Found in Text Mining only
Rhabdomyolysis	Rhabdomyolysis	Pubtator	32978841	Associate	★☆☆☆☆ Found in Text Mining only
Rheumatic Heart Disease	Rheumatic Heart Disease	BEFREE	3157636		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	3157636		★☆☆☆☆ Found in Text Mining only
Scleroderma	Scleroderma	BEFREE	3157636		★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxias	Spinocerebellar ataxia	Pubtator	25288802	Associate	★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	HPO_DG			★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	3157636		★☆☆☆☆ Found in Text Mining only
Teratoma	Teratoma	BEFREE	6961419		★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	35924232	Associate	★☆☆☆☆ Found in Text Mining only