PGM5

Chr 9

phosphoglucomutase 5

Also known as: PGMRP

NCBI Gene: 5239ENSG00000154330UniProt: Q15124

Phosphoglucomutases (EC 5.2.2.2.), such as PGM5, are phosphotransferases involved in interconversion of glucose-1-phosphate and glucose-6-phosphate. PGM activity is essential in formation of carbohydrates from glucose-6-phosphate and in formation of glucose-6-phosphate from galactose and glycogen (Edwards et al., 1995 [PubMed 8586438]).[supplied by OMIM, Mar 2008]

159
ClinVar variants
40
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— PGM5
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
40 Pathogenic / Likely Pathogenic· 97 VUS of 159 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.66LOEUF
pLI 0.001
Z-score 2.88
OE 0.39 (0.24–0.66)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.80Z-score
OE missense 0.87 (0.79–0.96)
278 obs / 318.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.39 (0.24–0.66)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.87 (0.79–0.96)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.95
0≤1.21.6
LoF obs/exp: 10 / 25.8Missense obs/exp: 278 / 318.0Syn Z: 0.40

ClinVar Variant Classifications

159 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic34
Likely Pathogenic6
VUS97
Likely Benign5
Benign2
34
Pathogenic
6
Likely Pathogenic
97
VUS
5
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
34
0
34
Likely Pathogenic
0
0
6
0
6
VUS
0
93
4
0
97
Likely Benign
0
3
0
2
5
Benign
0
0
1
1
2
Total096453144

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PGM5 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
p53-induced long non-coding RNA PGM5-AS1 inhibits the progression of esophageal squamous cell carcinoma through regulating miR-466/PTEN axis.
Zhihua Z et al.·IUBMB Life
2019
LncRNA PGM5-AS1 regulates cell functions and acts as a potential biomarker to predict prognosis in breast cancer.
Xiang L et al.·Int J Biol Markers
2025
Down-regulation of long noncoding RNA PGM5-AS1 correlates with tumor progression and predicts poor prognosis in clear cell renal cell carcinoma.
Qian M et al.·Eur Rev Med Pharmacol Sci
2019
Integrated plasma and exosome long noncoding RNA profiling is promising for diagnosing non-small cell lung cancer.
Wang N et al.·Clin Chem Lab Med
2023
A bioinformatics analysis: ZFHX4 is associated with metastasis and poor survival in ovarian cancer.
Zong S et al.·J Ovarian Res
2022
Network module function enrichment analysis of lung squamous cell carcinoma and lung adenocarcinoma.
Li P et al.·Medicine (Baltimore)
2022
Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-D-phosphohexomutase superfamily.
Backe PH et al.·Sci Rep
2020
Aciculin interacts with filamin C and Xin and is essential for myofibril assembly, remodeling and maintenance.
Molt S et al.·J Cell Sci
2014Functional
Transcriptomic analysis of high-throughput sequencing about circRNA, lncRNA and mRNA in bladder cancer.
Li M et al.·Gene
2018
Transcriptional Profiling of Human Peripheral Blood Mononuclear Cells Identifies Diagnostic Biomarkers That Distinguish Active and Latent Tuberculosis.
Wang S et al.·Front Immunol
2019Clinical trial
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools