PIGC
Basic information
Region (hg38): 1:172370189-172444086
Links
Phenotypes
GenCC
Source:
- glycosylphosphatidylinositol biosynthesis defect 16 (Limited), mode of inheritance: AR
- glycosylphosphatidylinositol biosynthesis defect 16 (Strong), mode of inheritance: AR
- autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Glycosylphosphatidylinositol biosynthesis defect 16 | 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 | Neurologic | 27694521 |
ClinVar
This is a list of variants' phenotypes submitted to
- Glycosylphosphatidylinositol biosynthesis defect 16 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGC 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 | 10 | |||||
missense | 42 | 46 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 3 | |||||
Total | 1 | 4 | 46 | 8 | 4 |
Variants in PIGC
This is a list of pathogenic ClinVar variants found in the PIGC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-172379094-G-A | not specified | Uncertain significance (Jan 25, 2023) | ||
1-172379114-A-G | not specified | Uncertain significance (Aug 14, 2023) | ||
1-172379120-A-C | not specified | Uncertain significance (Oct 05, 2022) | ||
1-172379180-A-C | not specified | Uncertain significance (Mar 02, 2023) | ||
1-172379182-C-T | Benign (Dec 31, 2019) | |||
1-172387173-A-G | not specified | Uncertain significance (Aug 21, 2024) | ||
1-172387201-G-A | not specified | Uncertain significance (Jul 25, 2023) | ||
1-172387218-A-T | not specified | Uncertain significance (Jun 17, 2024) | ||
1-172387229-C-T | not specified | Uncertain significance (Oct 17, 2023) | ||
1-172387271-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
1-172387304-G-T | not specified | Uncertain significance (Oct 19, 2024) | ||
1-172387314-C-T | not specified | Uncertain significance (Aug 26, 2024) | ||
1-172387323-C-G | not specified | Uncertain significance (Dec 12, 2023) | ||
1-172387325-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
1-172388595-A-G | not specified | Uncertain significance (Mar 26, 2024) | ||
1-172388622-C-T | not specified | Uncertain significance (Jul 08, 2022) | ||
1-172388645-C-T | Likely benign (Feb 01, 2023) | |||
1-172388679-C-A | not specified | Uncertain significance (Oct 30, 2023) | ||
1-172388682-C-A | not specified | Uncertain significance (Jan 02, 2024) | ||
1-172388703-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
1-172388786-G-A | Benign (Dec 14, 2017) | |||
1-172407773-C-T | not specified | Uncertain significance (Jul 07, 2024) | ||
1-172407783-C-T | not specified | Uncertain significance (Oct 29, 2024) | ||
1-172407798-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
1-172441742-C-A | Glycosylphosphatidylinositol biosynthesis defect 16 | Uncertain significance (Sep 22, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PIGC | protein_coding | protein_coding | ENST00000367728 | 1 | 73902 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00551 | 0.905 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.788 | 137 | 166 | 0.828 | 0.00000880 | 1915 |
Missense in Polyphen | 37 | 50.25 | 0.73632 | 650 | ||
Synonymous | 2.34 | 40 | 63.8 | 0.627 | 0.00000293 | 626 |
Loss of Function | 1.46 | 5 | 9.95 | 0.502 | 5.91e-7 | 105 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in GPI anchor biosynthesis (PubMed:8806613, PubMed:27694521). Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis (ECO:0000269|PubMed:27694521). {ECO:0000269|PubMed:27694521, ECO:0000269|PubMed:8806613}.;
- Disease
- DISEASE: Glycosylphosphatidylinositol biosynthesis defect 16 (GPIBD16) [MIM:617816]: An autosomal recessive disorder characterized by delayed psychomotor development, intellectual disability, and seizures. {ECO:0000269|PubMed:27694521}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);Synthesis of glycosylphosphatidylinositol (GPI);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Phosphatidylinositol phosphate metabolism
(Consensus)
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- loftool
- 0.918
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.22
Haploinsufficiency Scores
- pHI
- 0.313
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.592
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.917
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | High | Medium | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Pigc
- Phenotype
Gene ontology
- Biological process
- GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane
- Cellular component
- glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex;endoplasmic reticulum membrane;integral component of membrane
- Molecular function
- catalytic activity;phosphatidylinositol N-acetylglucosaminyltransferase activity