PGM2
protein-codingphosphoglucomutase 2
Gene summary
Enables phosphoglucomutase activity and phosphopentomutase activity. Predicted to be involved in purine ribonucleoside salvage. Predicted to act upstream of or within glucose metabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PGM2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018290.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 1 | 4 | ||
| missense | 78 | 3 | 1 | 82 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 84 | 4 | 2 | 90 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060760.2 | 14 | MANE Select | |
| Ensembl | ENSP00000371393.4 | 14 | MANE Select | |
| Ensembl | ENSP00000423269.1 | 5 | Standard | |
| Ensembl | ENSP00000422785.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycolysis / Gluconeogenesis - Homo sapiens (human)
- Starch and sucrose metabolism - Homo sapiens (human)
- Purine metabolism - Homo sapiens (human)
- Galactose metabolism - Homo sapiens (human)
- Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
Biological Process
- glycogen biosynthetic process
- glycogen catabolic process
- glucose metabolic process
- pentose-phosphate shunt
- galactose catabolic process
Molecular Function
- magnesium ion binding
- phosphoglucomutase activity
- protein binding
- phosphopentomutase activity
Cellular Component
- extracellular region
- cytosol
- secretory granule lumen
- extracellular exosome
- ficolin-1-rich granule lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381967
- Coding exons
- 14
- Length
- 36304
- Individuals with no LoFs
- 125651
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 97
- Defined
- 125748
- p
- 0.000386
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.376 | 307 | 326 | 0.941 | 0.0000164 | 4049 |
| Missense (PolyPhen) | 93 | 101.97 | 0.912 | 1218 | ||
| Synonymous | 0.816 | 111 | 122 | 0.906 | 0.00000686 | 1130 |
| Loss of Function | 1.75 | 23 | 34.0 | 0.676 | 0.00000199 | 382 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00081 | 0.00078 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00039 | 0.00039 | rare |
| South Asian | 0.00027 | 0.00026 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. May also catalyze the interconversion of glucose-1-phosphate and glucose-6-phosphate. Has low glucose 1,6-bisphosphate synthase activity. {ECO:0000269|PubMed:17804405}.;
Recessive Scores
- pRec
- 0.404
Intolerance Scores
- LoFtool
- 0.790
- RVIS EVS
- 0.09
- RVIS percentile EVS
- 60.65
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.850
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |