PGM3

phosphoglucomutase 3

Basic information

Region (hg38): 6:83147323-83193936

Links

ENSG00000013375 ∙ NCBI:5238 ∙ OMIM:172100 ∙ HGNC:8907 ∙ Uniprot:O95394 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 23 (Definitive), mode of inheritance: AR
• immunodeficiency 23 (Strong), mode of inheritance: AR
• immunodeficiency 23 (Supportive), mode of inheritance: AR
• immunodeficiency 23 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 23	AR	Allergy/Immunology/Infectious; Oncologic	Individuals are susceptible to recurrent and severe viral, bacterial, and fungal infections (as well as sequelae such as EBV-related lymphoma), and and prophylaxis, as well as prompt and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Oncologic	14981714; 24589341; 24698316; 24931394

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGM3 gene.

• Immunodeficiency 23 (328 variants)
• not provided (35 variants)
• Inborn genetic diseases (27 variants)
• not specified (6 variants)
• Severe combined immunodeficiency disease (4 variants)
• PGM3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGM3 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	68	3	72
missense	2	1	123	4	2	132
nonsense	4	1				5
start loss						0
frameshift	11	2				13
inframe indel	1		1			2
splice donor/acceptor (+/-2bp)		3	1			4
splice region			10	16	1	27
non coding	3	1	24	60	16	104
Total	21	8	150	132	21

Highest pathogenic variant AF is 0.0000395

Variants in PGM3

This is a list of pathogenic ClinVar variants found in the PGM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-83151959-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-83151982-C-A		not specified	Uncertain significance (Mar 11, 2024)
6-83152001-G-A		not specified	Uncertain significance (May 31, 2023)
6-83152312-C-A		not specified	Uncertain significance (Apr 13, 2022)
6-83152326-C-A		not specified	Uncertain significance (May 17, 2023)
6-83152365-G-A		not specified	Uncertain significance (Mar 08, 2024)
6-83153503-T-C			Likely benign (May 01, 2022)
6-83154033-T-C		not specified	Uncertain significance (Feb 01, 2023)
6-83154185-G-A		not specified	Uncertain significance (Apr 07, 2023)
6-83155954-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-83158615-A-G		not specified	Uncertain significance (Jan 03, 2024)
6-83159863-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-83159885-A-G		not specified	Uncertain significance (Nov 30, 2022)
6-83159890-T-C		not specified	Uncertain significance (Jul 19, 2023)
6-83166476-A-C		PGM3-related disorder	Likely benign (Jan 08, 2020)
6-83166527-AAAAT-A			Benign (Jul 30, 2020)
6-83166558-CA-C			Benign (Mar 13, 2020)
6-83166744-A-G			Likely benign (Aug 06, 2019)
6-83167937-G-A		not specified	Uncertain significance (Mar 21, 2023)
6-83169237-G-T		Immunodeficiency 23	Uncertain significance (May 29, 2022)
6-83169246-T-C		Immunodeficiency 23	Likely benign (Apr 16, 2023)
6-83169249-G-C		Immunodeficiency 23	Likely benign (Sep 08, 2023)
6-83169251-G-T		not specified • Immunodeficiency 23	Uncertain significance (Oct 17, 2022)
6-83169253-C-A		Immunodeficiency 23	Uncertain significance (Jan 28, 2020)
6-83169262-A-G		Immunodeficiency 23	Uncertain significance (Aug 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGM3	protein_coding	protein_coding	ENST00000506587	13	32787

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000146	1.00	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	227	301	0.755	0.0000144	3718
Missense in Polyphen		64	123.77	0.51707		1499
Synonymous	0.356	103	108	0.956	0.00000543	1087
Loss of Function	3.12	14	33.5	0.418	0.00000179	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000299	0.000299
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.000490	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc, a sugar nucleotide critical to multiple glycosylation pathways including protein N- and O-glycosylation. {ECO:0000303|PubMed:24589341, ECO:0000303|PubMed:24698316, ECO:0000303|PubMed:24931394}.
• Pathway: UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II;Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;Glucuronidation;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;UDP-<i>N</i>-acetyl-D-glucosamine biosynthesis II;Synthesis of UDP-N-acetyl-glucosamine;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.671

Intolerance Scores

• loftool: 0.794
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.644
• hipred: Y
• hipred_score: 0.544
• ghis: 0.552

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgm3
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; immune system phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;glucosamine metabolic process;UDP-N-acetylglucosamine biosynthetic process;protein N-linked glycosylation;protein O-linked glycosylation;spermatogenesis;glucose 1-phosphate metabolic process;hemopoiesis
• Cellular component: cellular_component;cytosol
• Molecular function: magnesium ion binding;phosphoacetylglucosamine mutase activity;phosphoglucomutase activity