PGM2L1
Basic information
Region (hg38): 11:74330315-74398433
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
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
- not provided (25 variants)
- Inborn genetic diseases (12 variants)
- Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities (3 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 | |||||
missense | 10 | 13 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 16 | 16 | ||||
Total | 6 | 0 | 11 | 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) | |||
11-74338524-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) | |||
11-74342502-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) | ||
11-74343130-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) | |||
11-74346602-T-C | Benign (May 14, 2021) | |||
11-74346742-G-A | Inborn genetic diseases | Uncertain significance (May 18, 2023) | ||
11-74346767-A-C | Inborn genetic diseases | Uncertain significance (Oct 06, 2021) | ||
11-74346886-C-T | Benign (May 14, 2021) | |||
11-74347203-T-C | Inborn genetic diseases | Uncertain significance (Jan 06, 2023) | ||
11-74351303-ACACTTTTTAT-A | Benign (May 26, 2021) |
GnomAD
Source:
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:
- 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