PGM2

phosphoglucomutase 2

Basic information

Region (hg38): 4:37826659-37862937

Links

ENSG00000169299 ∙ NCBI:55276 ∙ OMIM:172000 ∙ HGNC:8906 ∙ Uniprot:Q96G03 ∙ 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 PGM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGM2 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
missense			26	2	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	2	2

Variants in PGM2

This is a list of pathogenic ClinVar variants found in the PGM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-37826760-G-C		not specified	Uncertain significance (Aug 16, 2021)
4-37829982-G-A			Benign (Jul 15, 2018)
4-37830025-G-A		not specified	Likely benign (Jan 26, 2023)
4-37830081-G-A		not specified	Uncertain significance (Aug 17, 2021)
4-37834613-T-C			Likely benign (Nov 01, 2022)
4-37834691-G-A		not specified	Uncertain significance (Sep 17, 2021)
4-37837542-G-A		not specified	Uncertain significance (May 17, 2023)
4-37839917-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-37840069-T-C		not specified	Uncertain significance (Jun 27, 2023)
4-37840099-C-T		not specified	Uncertain significance (May 07, 2024)
4-37840202-C-T		not specified	Uncertain significance (May 09, 2023)
4-37840217-A-G			Likely benign (Nov 01, 2022)
4-37844383-A-G		not specified	Uncertain significance (Jan 26, 2023)
4-37844422-C-T		not specified	Uncertain significance (Feb 26, 2024)
4-37844452-T-C		not specified	Uncertain significance (Nov 08, 2022)
4-37844495-C-T		not specified	Uncertain significance (Apr 17, 2024)
4-37844501-C-T		not specified	Uncertain significance (May 15, 2024)
4-37845689-C-T			Benign (Apr 04, 2018)
4-37846944-G-T		not specified	Uncertain significance (Feb 03, 2022)
4-37846995-T-C		not specified	Uncertain significance (Jan 17, 2024)
4-37847019-C-T		not specified	Uncertain significance (Jun 11, 2021)
4-37847038-C-T		not specified	Uncertain significance (Dec 06, 2022)
4-37847058-G-A		not specified	Uncertain significance (Nov 07, 2023)
4-37847071-T-C		not specified	Uncertain significance (May 30, 2024)
4-37847077-G-A		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGM2	protein_coding	protein_coding	ENST00000381967	14	36304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-12	0.798	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.376	307	326	0.941	0.0000164	4049
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000383	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000393	0.000387
Middle Eastern	0.000383	0.000381
South Asian	0.000272	0.000261
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: 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);Pentose phosphate pathway - Homo sapiens (human);Pathways in clear cell renal cell carcinoma;Glucuronidation;Neutrophil degranulation;Pentose phosphate pathway (hexose monophosphate shunt);purine ribonucleosides degradation to ribose-1-phosphate;Metabolism of carbohydrates;Fructose Mannose metabolism;glycogenolysis;Innate Immune System;Immune System;Metabolism;2,-deoxy-α-D-ribose 1-phosphate degradation;D-galactose degradation V (Leloir pathway);Galactose catabolism;GDP-glucose biosynthesis II;glycogen biosynthesis;Glycogen breakdown (glycogenolysis);Glycogen synthesis;Glycogen metabolism (Consensus)

Recessive Scores

• pRec: 0.404

Intolerance Scores

• loftool: 0.790
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.65

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.294
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgm2
• Phenotype: normal phenotype

Gene ontology

• Biological process: glycogen biosynthetic process;glycogen catabolic process;glucose metabolic process;pentose-phosphate shunt;galactose catabolic process;neutrophil degranulation;deoxyribose phosphate catabolic process
• Cellular component: extracellular region;cytosol;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: magnesium ion binding;phosphoglucomutase activity;protein binding;phosphopentomutase activity