PGM5

Summary

PGM5 (phosphoglucomutase 5, HGNC:8908) is a protein-coding gene on chromosome 9q21.11, encoding Phosphoglucomutase-like protein 5 (Q15124). Component of adherens-type cell-cell and cell-matrix junctions.

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]).

Source: NCBI Gene 5239 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 117 total
• MANE Select transcript: NM_021965

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8908
Approved symbol	PGM5
Name	phosphoglucomutase 5
Location	9q21.11
Locus type	gene with protein product
Status	Approved
Aliases	PGMRP
Ensembl gene	ENSG00000154330
Ensembl biotype	protein_coding
OMIM	600981
Entrez	5239

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000396392, ENST00000396396, ENST00000431583, ENST00000472639, ENST00000496758, ENST00000587852, ENST00000604870, ENST00000902465, ENST00000902466, ENST00000902467, ENST00000902468, ENST00000902469

RefSeq mRNA: 1 — MANE Select: NM_021965 NM_021965

CCDS: CCDS6622

Canonical transcript exons

ENST00000396396 — 11 exons

Exon	Start	End
ENSE00001767423	68499227	68499361
ENSE00003504676	68378199	68378361
ENSE00003524273	68387463	68387588
ENSE00003529213	68392319	68392473
ENSE00003550830	68529567	68531061
ENSE00003553778	68391534	68391724
ENSE00003571012	68483865	68484048
ENSE00003618508	68479418	68479553
ENSE00003619857	68465093	68465208
ENSE00003681820	68384398	68384544
ENSE00003848872	68356611	68357388

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 99.00.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8308 / max 200.0442, expressed in 354 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96786	1.1985	261
205504	0.2824	150
96787	0.2643	152
205505	0.0856	53

Top tissues by expression

284 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
saphenous vein	UBERON:0007318	99.00	gold quality
cauda epididymis	UBERON:0004360	98.74	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.59	gold quality
lower esophagus	UBERON:0013473	98.53	gold quality
seminal vesicle	UBERON:0000998	98.22	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.21	gold quality
body of uterus	UBERON:0009853	98.11	gold quality
mucosa of stomach	UBERON:0001199	98.07	gold quality
urethra	UBERON:0000057	98.05	gold quality
vena cava	UBERON:0004087	97.91	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.89	gold quality
right atrium auricular region	UBERON:0006631	97.57	gold quality
left uterine tube	UBERON:0001303	97.45	gold quality
popliteal artery	UBERON:0002250	97.26	gold quality
tibial artery	UBERON:0007610	97.25	gold quality
heart right ventricle	UBERON:0002080	96.95	gold quality
nipple	UBERON:0002030	96.90	gold quality
cardiac atrium	UBERON:0002081	96.86	gold quality
right coronary artery	UBERON:0001625	96.78	gold quality
buccal mucosa cell	CL:0002336	96.27	gold quality
aorta	UBERON:0000947	96.20	gold quality
heart	UBERON:0000948	95.84	gold quality
apex of heart	UBERON:0002098	95.83	gold quality
coronary artery	UBERON:0001621	95.74	gold quality
descending thoracic aorta	UBERON:0002345	95.74	gold quality
smooth muscle tissue	UBERON:0001135	95.70	gold quality
colonic epithelium	UBERON:0000397	95.69	gold quality
myometrium	UBERON:0001296	95.58	gold quality
left coronary artery	UBERON:0001626	95.58	gold quality
cardiac ventricle	UBERON:0002082	95.39	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.97
E-GEOD-81383	no	42.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting PGM5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4804-3P	99.65	67.78	866
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-766-5P	99.47	67.91	2225

Literature-anchored findings (GeneRIF, showing 1)

• Aciculin interacts with filamin C and Xin and is essential for myofibril assembly. (PMID:24963132)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pgm5	ENSDARG00000060745
mus_musculus	Pgm5	ENSMUSG00000041731
rattus_norvegicus	Pgm5	ENSRNOG00000015406
drosophila_melanogaster	Pgm1	FBGN0003076
caenorhabditis_elegans		WBGENE00019890

Paralogs (6): PGM3 (ENSG00000013375), PGM1 (ENSG00000079739), PRTFDC1 (ENSG00000099256), PGM2L1 (ENSG00000165434), HPRT1 (ENSG00000165704), PGM2 (ENSG00000169299)

Protein

Protein identifiers

Phosphoglucomutase-like protein 5 — Q15124 (reviewed: Q15124)

Alternative names: Aciculin, Phosphoglucomutase-related protein

All UniProt accessions (2): Q15124, Q5JTY7

UniProt curated annotations — full annotation on UniProt →

Function. Component of adherens-type cell-cell and cell-matrix junctions. Positively regulates maturation and alignment of myofibrils, also promotes organization of sarcomeres. Has no phosphoglucomutase activity in vitro.

Subunit / interactions. Interacts with DMD/dystrophin; the interaction is direct. Interacts with UTRN/utrophin. Interacts (via N-terminus) with XIRP1 isoform B (XinB) or FLNC (via repeats 18 to 21); the interactions are competitive and do not form a ternary complex.

Subcellular location. Cell junction. Adherens junction. Cytoplasm. Cytoskeleton. Cell membrane. Sarcolemma.

Tissue specificity. Detected in smooth and cardiac muscle at high levels and in skeletal muscle at low level. Present in other tissues due to vascular or other smooth muscle component. Low levels are present in liver, kidney, skin and brain (at protein level).

Similarity. Belongs to the phosphohexose mutase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q15124-1	1	yes
Q15124-2	2

RefSeq proteins (1): NP_068800* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005841	Alpha-D-phosphohexomutase_SF	Family
IPR005844	A-D-PHexomutase_a/b/a-I	Domain
IPR005845	A-D-PHexomutase_a/b/a-II	Domain
IPR005846	A-D-PHexomutase_a/b/a-III	Domain
IPR016055	A-D-PHexomutase_a/b/a-I/II/III	Homologous_superfamily
IPR016066	A-D-PHexomutase_CS	Conserved_site
IPR036900	A-D-PHexomutase_C_sf	Homologous_superfamily
IPR045244	PGM	Family

Pfam: PF02878, PF02879, PF02880, PF24947

UniProt features (10 total): sequence conflict 3, region of interest 2, modified residue 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7U21	X-RAY DIFFRACTION	1.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15124-F1	96.55	0.96

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 120, 122

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 131 (showing top): GOBP_MUSCLE_TISSUE_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GCANCTGNY_MYOD_Q6, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, CHANDRAN_METASTASIS_DN, INAMURA_LUNG_CANCER_SCC_DN, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, INGRAM_SHH_TARGETS_DN, GOBP_ACTOMYOSIN_STRUCTURE_ORGANIZATION, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_ORGANELLE_ASSEMBLY, LINDVALL_IMMORTALIZED_BY_TERT_UP, GOCC_CELL_CELL_JUNCTION, GOBP_MUSCLE_CELL_DEVELOPMENT

GO Biological Process (4): carbohydrate metabolic process (GO:0005975), cell adhesion (GO:0007155), striated muscle tissue development (GO:0014706), myofibril assembly (GO:0030239)

GO Molecular Function (4): magnesium ion binding (GO:0000287), structural molecule activity (GO:0005198), intramolecular phosphotransferase activity (GO:0016868), phosphoglucomutase activity (GO:0004614)

GO Cellular Component (17): stress fiber (GO:0001725), cytosol (GO:0005829), adherens junction (GO:0005912), spot adherens junction (GO:0005914), focal adhesion (GO:0005925), cytoplasmic side of plasma membrane (GO:0009898), intercalated disc (GO:0014704), dystrophin-associated glycoprotein complex (GO:0016010), Z disc (GO:0030018), cell-substrate junction (GO:0030055), sarcolemma (GO:0042383), costamere (GO:0043034), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), membrane (GO:0016020), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
plasma membrane	2
primary metabolic process	1
cellular process	1
muscle tissue development	1
cellular component assembly involved in morphogenesis	1
actomyosin structure organization	1
striated muscle cell development	1
supramolecular fiber organization	1
membraneless organelle assembly	1
metal ion binding	1
molecular_function	1
intramolecular transferase activity	1
intramolecular phosphotransferase activity	1
actomyosin	1
contractile actin filament bundle	1
cytoplasm	1
cell-cell junction	1
adherens junction	1
cell-substrate junction	1
cytoplasmic side of membrane	1
cell-cell contact zone	1
glycoprotein complex	1
plasma membrane protein complex	1
I band	1
anchoring junction	1
myofibril	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
membrane	1
cell periphery	1
cell junction	1

Protein interactions and networks

STRING

1798 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PGM5	PGM2	Q96G03	909
PGM5	PGM3	O95394	886
PGM5	FLNC	Q14315	587
PGM5	XIRP1	Q702N8	572
PGM5	PGM2L1	Q6PCE3	571
PGM5	SYNPO2	Q9UMS6	568
PGM5	MYOT	Q9UBF9	565
PGM5	MYOZ1	Q9NP98	548
PGM5	ASS1	P00966	516
PGM5	GBE1	Q04446	505
PGM5	SYNM	O15061	452
PGM5	UGP2	Q16851	449
PGM5	LMBRD2	Q68DH5	398
PGM5	KEAP1	Q14145	398
PGM5	GPI	P06744	397

IntAct

0 interactions, top by confidence:

BioGRID (9): GPI (Co-fractionation), GYG1 (Co-fractionation), HSPE1 (Co-fractionation), PGM3 (Co-fractionation), PGM5 (Co-fractionation), PGM5 (Co-fractionation), TALDO1 (Co-fractionation), UTRN (Affinity Capture-Western), VCL (Co-fractionation)

ESM2 similar proteins: A3KG59, A4IFH5, B9N1F9, D3ZVR9, O04059, O35331, O35621, O46560, P11172, P24298, P37111, Q03154, Q04609, Q15124, Q17QK3, Q2R483, Q501L1, Q5E9T8, Q5I0K3, Q5NAY4, Q5R514, Q5R5C9, Q5RDE7, Q5RDN7, Q5RFB0, Q5RFI8, Q6AY30, Q6AYS7, Q6K2E8, Q6PTT0, Q6Q0N1, Q6ZV70, Q7TSV4, Q7X7L3, Q8BZF8, Q8CG45, Q8CG76, Q8IYS1, Q8K183, Q8N0X4

Diamond homologs: A0A2R6W0K6, D3ZVR9, O02606, O15820, O18719, O49299, O74374, P00949, P33401, P36871, P37012, P38652, P39671, P47244, P57749, P93262, P93804, P93805, Q08DP0, Q116W4, Q15124, Q23919, Q4R5E4, Q4WY53, Q890U1, Q8BZF8, Q97LS0, Q9D0F9, Q9M4G4, Q9M4G5, Q9P931, Q9SCY0, Q9SGC1, Q9SM59, Q9SM60, Q9SMM0, Q9SNX2, Q9VUY9, Q9ZSQ4, A0KNE8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

117 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	95
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2564 predictions. Top by Δscore:

Variant	Effect	Δscore
9:68357386:GGG:G	donor_gain	1.0000
9:68357387:GG:G	donor_gain	1.0000
9:68357387:GGG:G	donor_gain	1.0000
9:68357387:GGGT:G	donor_loss	1.0000
9:68357388:GG:G	donor_gain	1.0000
9:68357388:GGT:G	donor_loss	1.0000
9:68357389:G:GG	donor_gain	1.0000
9:68357389:GT:G	donor_loss	1.0000
9:68357390:T:A	donor_loss	1.0000
9:68357391:G:GG	donor_loss	1.0000
9:68359051:G:GT	donor_gain	1.0000
9:68384390:C:G	acceptor_gain	1.0000
9:68384391:A:AG	acceptor_gain	1.0000
9:68384394:TTA:T	acceptor_loss	1.0000
9:68384395:TA:T	acceptor_loss	1.0000
9:68384396:AGGT:A	acceptor_loss	1.0000
9:68384500:G:GT	donor_gain	1.0000
9:68384540:CAGAG:C	donor_loss	1.0000
9:68384541:AGAGG:A	donor_loss	1.0000
9:68384542:GAG:G	donor_gain	1.0000
9:68384542:GAGG:G	donor_loss	1.0000
9:68384543:AGGTA:A	donor_loss	1.0000
9:68384544:GGT:G	donor_loss	1.0000
9:68384545:G:C	donor_loss	1.0000
9:68384546:T:A	donor_loss	1.0000
9:68387455:A:AG	acceptor_gain	1.0000
9:68387456:T:G	acceptor_gain	1.0000
9:68387459:TTAG:T	acceptor_loss	1.0000
9:68387461:A:AG	acceptor_gain	1.0000
9:68387461:AGT:A	acceptor_gain	1.0000

AlphaMissense

3698 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:68357381:C:A	A85D	0.998
9:68378209:T:C	L91P	0.998
9:68357266:A:C	S47R	0.996
9:68357268:C:A	S47R	0.996
9:68357268:C:G	S47R	0.996
9:68357374:G:C	A83P	0.996
9:68357378:C:A	A84E	0.996
9:68384439:A:C	S156R	0.996
9:68384441:C:A	S156R	0.996
9:68384441:C:G	S156R	0.996
9:68357375:C:A	A83D	0.995
9:68357380:G:C	A85P	0.995
9:68479465:T:A	W403R	0.995
9:68479465:T:C	W403R	0.995
9:68378284:G:A	G116E	0.994
9:68384466:T:C	C165R	0.994
9:68357320:G:C	G65R	0.993
9:68357333:G:T	R69M	0.993
9:68357377:G:C	A84P	0.993
9:68384468:T:G	C165W	0.993
9:68357315:T:A	V63E	0.992
9:68378218:G:A	G94E	0.992
9:68392457:A:C	S343R	0.992
9:68392459:C:A	S343R	0.992
9:68392459:C:G	S343R	0.992
9:68499258:G:C	R504P	0.992
9:68529595:C:A	A548E	0.992
9:68357318:T:A	V64E	0.991
9:68378209:T:G	L91R	0.991
9:68378283:G:A	G116R	0.991

dbSNP variants (sampled 300 via entrez): RS1000011957 (9:68518228 G>A), RS1000021110 (9:68517176 G>A,T), RS1000037025 (9:68481747 A>T), RS1000063338 (9:68473630 T>C), RS1000179827 (9:68480178 C>T), RS1000196453 (9:68498583 T>C), RS1000291001 (9:68426098 A>T), RS1000292189 (9:68463310 G>A), RS1000356729 (9:68420395 A>G), RS1000366634 (9:68420189 G>A,T), RS1000379201 (9:68475374 C>T), RS1000425393 (9:68469245 A>G), RS1000481896 (9:68523161 A>G), RS1000579748 (9:68457797 A>G), RS1000627292 (9:68506939 C>A,T)

Disease associations

OMIM: gene MIM:600981 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001647_8	Bipolar disorder	5.000000e-06
GCST009391_2107	Metabolite levels	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010373	phosphatidylcholine 32:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, decreases methylation, increases expression, affects cotreatment	5
mercuric bromide	decreases expression, affects cotreatment	2
Benzo(a)pyrene	decreases methylation, affects methylation	2
Nickel	decreases expression	2
Tretinoin	decreases expression, increases expression	2
FR900359	increases phosphorylation	1
2,4,6-tribromophenol	increases expression	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
methylselenic acid	increases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
trichostatin A	decreases expression	1
sulforaphane	decreases expression	1
sodium arsenite	decreases expression, increases abundance	1
tobacco tar	decreases reaction, increases expression	1
diallyl disulfide	decreases reaction, increases expression	1
aflatoxin B2	increases methylation	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
incobotulinumtoxinA	decreases expression	1
Zoledronic Acid	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	decreases expression, increases abundance	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.