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 with hypotonia, dysmorphic facies, and skin abnormalities (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.

Inborn_genetic_diseases (47 variants)
not_provided (13 variants)
Neurodevelopmental_disorder_with_hypotonia,_dysmorphic_facies,_and_skin_abnormalities (5 variants)
PGM2L1-related_disorder (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. These statistics are base on transcript: NM_000173582.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			45 clinvar	2 clinvar		47
nonsense	3 clinvar					3
start loss						0
frameshift	5 clinvar					5
splice donor/acceptor (+/-2bp)						0
Total	8	0	45	4	0

Highest pathogenic variant AF is 0.0000171067

Loading clinvar variants...

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
Phenotype

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