PGGT1B
Basic information
Region (hg38): 5:115204011-115262877
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGGT1B 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 | 0 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in PGGT1B
This is a list of pathogenic ClinVar variants found in the PGGT1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-115212433-T-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 5-115212479-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
| 5-115221885-T-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 5-115221905-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 5-115237868-C-G | not specified | Uncertain significance (Oct 14, 2023) | ||
| 5-115241549-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
| 5-115253208-G-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 5-115253236-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 5-115262802-C-G | not specified | Uncertain significance (Aug 04, 2023) | ||
| 5-115262817-C-A | not specified | Uncertain significance (Jun 06, 2022) | ||
| 5-115262842-T-C | not specified | Uncertain significance (Jan 10, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PGGT1B | protein_coding | protein_coding | ENST00000419445 | 9 | 52043 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0408 | 0.958 | 125728 | 0 | 8 | 125736 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 157 | 197 | 0.798 | 0.00000938 | 2436 |
| Missense in Polyphen | 31 | 60.601 | 0.51154 | 795 | ||
| Synonymous | -0.393 | 76 | 71.8 | 1.06 | 0.00000346 | 716 |
| Loss of Function | 2.84 | 6 | 19.6 | 0.307 | 9.88e-7 | 249 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000216 | 0.000215 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000180 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to a cysteine at the fourth position from the C-terminus of proteins having the C-terminal sequence Cys-aliphatic-aliphatic-X. Known substrates include RAC1, RAC2, RAP1A and RAP1B. {ECO:0000269|PubMed:8106351}.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.422
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.66
Haploinsufficiency Scores
- pHI
- 0.560
- hipred
- Y
- hipred_score
- 0.530
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.442
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pggt1b
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; respiratory system phenotype; liver/biliary system 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); neoplasm; immune system phenotype;
Zebrafish Information Network
- Gene name
- pggt1b
- Affected structure
- muscle
- Phenotype tag
- abnormal
- Phenotype quality
- damaged
Gene ontology
- Biological process
- positive regulation of cell population proliferation;protein prenylation;protein geranylgeranylation;response to cytokine;positive regulation of cell cycle;negative regulation of nitric-oxide synthase biosynthetic process
- Cellular component
- CAAX-protein geranylgeranyltransferase complex
- Molecular function
- protein geranylgeranyltransferase activity;CAAX-protein geranylgeranyltransferase activity;drug binding;zinc ion binding;isoprenoid binding;peptide binding