PGM2L1

phosphoglucomutase 2 like 1

Basic information

Region (hg38): 11:74330316-74398433

Links

ENSG00000165434 ∙ NCBI:283209 ∙ OMIM:611610 ∙ HGNC:20898 ∙ Uniprot:Q6PCE3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities (Strong), mode of inheritance: AR
• neurodevelopmental disorder (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dermatologic; Musculoskeletal; Neurologic	33979636

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGM2L1 gene.

• not provided (5 variants)
• Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities (3 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGM2L1 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			24	1	2	27
nonsense	2					2
start loss						0
frameshift	4					4
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					16	16
Total	6	0	25	1	19

Variants in PGM2L1

This is a list of pathogenic ClinVar variants found in the PGM2L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74336638-A-G			Benign (May 14, 2021)
11-74336824-A-AT			Benign (May 26, 2021)
11-74338483-G-A		Inborn genetic diseases	Uncertain significance (Nov 09, 2024)
11-74338524-A-G			Benign (May 04, 2021)
11-74338579-C-T		Inborn genetic diseases	Uncertain significance (Nov 29, 2023)
11-74338763-G-A			Benign (May 14, 2021)
11-74342481-T-C		Inborn genetic diseases	Uncertain significance (Mar 05, 2025)
11-74342502-C-T			Benign (May 04, 2021)
11-74342507-C-T		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
11-74342508-G-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
11-74342528-G-A		PGM2L1-related disorder	Likely benign (Jan 20, 2022)
11-74342543-GGA-G		Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities	Pathogenic (Jan 11, 2023)
11-74342575-C-A		Inborn genetic diseases	Uncertain significance (Nov 08, 2021)
11-74342575-C-G		Inborn genetic diseases	Uncertain significance (May 12, 2024)
11-74342615-A-G		Inborn genetic diseases	Uncertain significance (Feb 20, 2025)
11-74342625-A-C		Inborn genetic diseases	Uncertain significance (Feb 07, 2025)
11-74342970-C-T		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
11-74343130-A-G			Benign (May 17, 2021)
11-74343301-G-T			Benign (May 14, 2021)
11-74343325-A-G		Inborn genetic diseases	Uncertain significance (Jan 19, 2022)
11-74343332-C-A		Inborn genetic diseases	Pathogenic (May 10, 2022)
11-74343353-C-A		Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities	Pathogenic (Nov 10, 2022)
11-74345482-CCTT-C			Uncertain significance (Aug 01, 2023)
11-74345571-AT-A		Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities	Pathogenic (Nov 10, 2022)
11-74345645-AAC-A			Pathogenic (Jul 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGM2L1	protein_coding	protein_coding	ENST00000298198	14	68156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0259	0.974	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	214	328	0.652	0.0000164	4088
Missense in Polyphen		84	141.61	0.59319		1701
Synonymous	1.14	98	113	0.864	0.00000537	1169
Loss of Function	3.72	9	31.5	0.285	0.00000150	411

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000301
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.0000544	0.0000544
South Asian	0.000104	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glucose 1,6-bisphosphate synthase using 1,3- bisphosphoglycerate as a phosphate donor and a series of 1- phosphate sugars as acceptors, including glucose 1-phosphate, mannose 1-phosphate, ribose 1-phosphate and deoxyribose 1- phosphate. 5 or 6-phosphosugars are bad substrates, with the exception of glucose 6-phosphate. Also synthesizes ribose 1,5- bisphosphate. Has only low phosphopentomutase and phosphoglucomutase activities. {ECO:0000269|PubMed:17804405, ECO:0000269|PubMed:18927083}.
• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Glycogen synthetase deficiency;Glycogenosis, Type III. Cori disease, Debrancher glycogenosis;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Starch and Sucrose Metabolism;Metabolism of carbohydrates;Metabolism;Glycolysis;Galactose catabolism;Glucose metabolism;Glycogen breakdown (glycogenolysis);Glycogen synthesis;Glycogen metabolism (Consensus)

Recessive Scores

• pRec: 0.204

Intolerance Scores

• loftool: 0.707
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• pHI: 0.445
• hipred: Y
• hipred_score: 0.639
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgm2l1

Gene ontology

• Biological process: glycogen biosynthetic process;glycogen catabolic process;galactose catabolic process;canonical glycolysis
• Cellular component: cytosol
• Molecular function: phosphoglucomutase activity;metal ion binding;glucose-1,6-bisphosphate synthase activity