PGAM1

phosphoglycerate mutase 1, the group of Bisphosphoglycerate phosphatases|Phosphoglycerate mutases

Basic information

Region (hg38): 10:97426191-97433444

Previous symbols: [ "PGAMA" ]

Links

ENSG00000171314 ∙ NCBI:5223 ∙ OMIM:172250 ∙ HGNC:8888 ∙ Uniprot:P18669 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGAM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGAM1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	3

Variants in PGAM1

This is a list of pathogenic ClinVar variants found in the PGAM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-97426318-A-G		not specified	Uncertain significance (Jan 19, 2024)
10-97426321-A-G			Benign (Dec 31, 2019)
10-97426341-G-A		not specified	Uncertain significance (Jul 12, 2023)
10-97426374-A-C		not specified	Uncertain significance (Oct 29, 2021)
10-97426384-A-G		not specified	Uncertain significance (Aug 12, 2021)
10-97430382-C-T		not specified	Uncertain significance (Jul 06, 2021)
10-97430394-T-C		not specified	Uncertain significance (Jan 18, 2022)
10-97430403-G-C		not specified	Uncertain significance (Nov 09, 2023)
10-97430432-C-T		not specified	Uncertain significance (Feb 07, 2025)
10-97430478-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-97430519-G-T		not specified	Uncertain significance (Dec 09, 2023)
10-97430528-G-A		not specified	Uncertain significance (May 02, 2024)
10-97430536-T-C			Benign (Jun 26, 2018)
10-97430538-A-T		not specified	Uncertain significance (Jul 30, 2024)
10-97430553-C-G		not specified	Uncertain significance (Feb 23, 2025)
10-97430595-A-G		not specified	Uncertain significance (Nov 14, 2024)
10-97430637-A-G		not specified	Uncertain significance (Apr 15, 2024)
10-97430996-C-T			Benign (Dec 31, 2019)
10-97431051-A-G		not specified	Uncertain significance (Mar 24, 2023)
10-97431118-T-C		not specified	Uncertain significance (Jul 14, 2023)
10-97431123-A-G		not specified	Uncertain significance (Sep 10, 2024)
10-97432357-C-G		not specified	Uncertain significance (Sep 08, 2024)
10-97432357-C-T		not specified	Uncertain significance (Jun 22, 2021)
10-97432391-C-T		not specified	Uncertain significance (Oct 13, 2023)
10-97432405-A-C		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGAM1	protein_coding	protein_coding	ENST00000334828	4	7282

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-7	0.169	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.314	136	147	0.927	0.00000849	1661
Missense in Polyphen		29	37.843	0.76633		540
Synonymous	-1.42	72	58.3	1.24	0.00000316	508
Loss of Function	-0.0473	10	9.84	1.02	4.39e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

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);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;Cori Cycle;Glycolysis and Gluconeogenesis;Neutrophil degranulation;Metabolism of carbohydrates;Glycolysis Gluconeogenesis;Glycolysis and Gluconeogenesis;TCR;Innate Immune System;Immune System;Metabolism;Rapoport-Luebering glycolytic shunt;Glycolysis;EGFR1;gluconeogenesis;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.303

Intolerance Scores

• loftool: 0.648
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.200
• hipred: Y
• hipred_score: 0.556
• ghis: 0.588

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgam1

Gene ontology

• Biological process: gluconeogenesis;glycolytic process;regulation of glycolytic process;neutrophil degranulation;regulation of pentose-phosphate shunt;respiratory burst;canonical glycolysis
• Cellular component: extracellular region;cytoplasm;cytosol;membrane;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: bisphosphoglycerate mutase activity;phosphoglycerate mutase activity;protein binding;hydrolase activity;protein kinase binding