PGAM2

phosphoglycerate mutase 2, the group of Phosphoglycerate mutases|Bisphosphoglycerate phosphatases

Basic information

Region (hg38): 7:44062727-44065567

Links

ENSG00000164708

∙ NCBI:5224 ∙ OMIM:612931 ∙ HGNC:8889 ∙ Uniprot:P15259 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

glycogen storage disease due to phosphoglycerate mutase deficiency (Strong), mode of inheritance: AR
glycogen storage disease due to phosphoglycerate mutase deficiency (Strong), mode of inheritance: AR
glycogen storage disease due to phosphoglycerate mutase deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Glycogen storage disease X	AR	Renal	Preventive measures to reduce the chance of severe sequelae can be beneficial, as individuals can present with exercise intolerance, and renal failure has been described	Biochemical; Musculoskeletal; Renal	6283419; 6262916; 6308514; 8447317; 10545043; 19273759

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGAM2 gene.

Glycogen_storage_disease_type_X (148 variants)
Inborn_genetic_diseases (52 variants)
not_provided (32 variants)
PGAM2-related_disorder (11 variants)
not_specified (6 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Rhabdomyolysis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGAM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000290.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	45 clinvar	2 clinvar	48
missense		2 clinvar	95 clinvar	6 clinvar	1 clinvar	104
nonsense	5 clinvar	1 clinvar				6
start loss						0
frameshift	2 clinvar	2 clinvar				4
splice donor/acceptor (+/-2bp)						0
Total	7	5	96	51	3

Highest pathogenic variant AF is 0.000382972

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGAM2	protein_coding	protein_coding	ENST00000297283	3	2861

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-7	0.118	125574	1	172	125747	0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.667	180	157	1.15	0.0000105	1647
Missense in Polyphen		78	68.633	1.1365		705
Synonymous	-0.651	70	63.4	1.10	0.00000432	500
Loss of Function	-0.287	10	9.07	1.10	3.97e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00789	0.00785
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Interconversion of 3- and 2-phosphoglycerate with 2,3- bisphosphoglycerate as the primer of the reaction. Can also catalyze the reaction of EC 5.4.2.4 (synthase), but with a reduced activity.;
Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Warburg Effect;Glycolysis;Glycogenosis, Type VII. Tarui disease;Gluconeogenesis;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Fanconi-bickel syndrome;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Glycogenosis, Type IB;Glycolysis and Gluconeogenesis;Metabolism of carbohydrates;Glycolysis Gluconeogenesis;Metabolism;Rapoport-Luebering glycolytic shunt;Glycolysis;gluconeogenesis;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

pRec: 0.215

Intolerance Scores

loftool: 0.468
rvis_EVS: -0.51
rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

pHI: 0.703
hipred: Y
hipred_score: 0.665
ghis: 0.445

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.997

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Pgam2
Phenotype

Zebrafish Information Network

Gene name: pgam2
Affected structure: fast muscle cell
Phenotype tag: abnormal
Phenotype quality: decreased diameter

Gene ontology

Biological process: gluconeogenesis;glycolytic process;striated muscle contraction;Notch signaling pathway;spermatogenesis;response to mercury ion;canonical glycolysis
Cellular component: nucleus;cytosol;extracellular exosome
Molecular function: bisphosphoglycerate mutase activity;phosphoglycerate mutase activity;hydrolase activity;2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity;cofactor binding