PGM5

phosphoglucomutase 5

Basic information

Region (hg38): 9:68328307-68531061

Links

ENSG00000154330 ∙ NCBI:5239 ∙ OMIM:600981 ∙ HGNC:8908 ∙ Uniprot:Q15124 ∙ 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 PGM5 gene.

• Inborn genetic diseases (37 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGM5 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				1	1	2
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	35	3	2

Variants in PGM5

This is a list of pathogenic ClinVar variants found in the PGM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-68357096-G-A			Benign (Jul 25, 2019)
9-68357167-G-A		not specified	Uncertain significance (Jun 30, 2022)
9-68357176-G-A		not specified	Uncertain significance (Nov 18, 2022)
9-68357179-G-C		not specified	Uncertain significance (Oct 29, 2021)
9-68357203-G-A		not specified	Uncertain significance (Dec 06, 2022)
9-68357221-G-A		not specified	Uncertain significance (Feb 15, 2023)
9-68357244-C-G		not specified	Uncertain significance (Jul 25, 2023)
9-68357313-G-T		not specified	Uncertain significance (May 23, 2023)
9-68357329-G-A		not specified	Uncertain significance (Aug 02, 2022)
9-68357348-C-A		not specified	Uncertain significance (Sep 29, 2023)
9-68378224-A-C		not specified	Uncertain significance (May 31, 2023)
9-68378237-G-A			Benign (Apr 04, 2018)
9-68378302-G-T		not specified	Uncertain significance (Feb 02, 2022)
9-68378303-C-T			Likely benign (Aug 05, 2018)
9-68384404-C-T		not specified	Uncertain significance (Jun 27, 2023)
9-68384440-G-A		not specified	Uncertain significance (Feb 28, 2023)
9-68384446-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-68384472-G-C		not specified	Uncertain significance (Feb 21, 2024)
9-68384488-T-C		not specified	Uncertain significance (Jun 29, 2023)
9-68384494-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-68384538-T-C		not specified	Uncertain significance (Jan 19, 2022)
9-68387468-A-G		not specified	Uncertain significance (Dec 15, 2023)
9-68387471-G-C		not specified	Uncertain significance (May 08, 2023)
9-68387504-C-T		not specified	Uncertain significance (Dec 03, 2021)
9-68387534-G-A		not specified	Likely benign (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGM5	protein_coding	protein_coding	ENST00000396396	11	202754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000591	0.998	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.798	278	318	0.874	0.0000174	3673
Missense in Polyphen		84	124.95	0.67227		1453
Synonymous	0.399	118	124	0.954	0.00000690	1154
Loss of Function	2.88	10	25.8	0.388	0.00000148	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000186
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of adherens-type cell-cell and cell-matrix junctions. Lacks phosphoglucomutase activity.
• Pathway: Glucuronidation (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.459
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.477
• hipred: Y
• hipred_score: 0.710
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.461

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgm5

Zebrafish Information Network

• Gene name: pgm5
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: detached from

Gene ontology

• Biological process: cell adhesion;striated muscle tissue development;myofibril assembly
• Cellular component: stress fiber;cytosol;cell-cell adherens junction;spot adherens junction;focal adhesion;cytoplasmic side of plasma membrane;intercalated disc;dystrophin-associated glycoprotein complex;Z disc;sarcolemma;costamere
• Molecular function: magnesium ion binding;phosphoglucomutase activity;structural molecule activity