PLAC8
Basic information
Region (hg38): 4:83059493-83137075
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 PLAC8 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 0 |
Variants in PLAC8
This is a list of pathogenic ClinVar variants found in the PLAC8 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-83066492-A-T | not specified | Uncertain significance (Jan 23, 2025) | ||
| 4-83075300-G-A | not specified | Uncertain significance (Nov 28, 2023) | ||
| 4-83075375-G-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 4-83094697-C-T | not specified | Likely benign (May 15, 2023) | ||
| 4-83094698-G-A | not specified | Uncertain significance (Nov 30, 2022) | ||
| 4-83094721-T-C | not specified | Uncertain significance (Jul 26, 2021) | ||
| 4-83107858-G-C | not specified | Uncertain significance (May 30, 2024) | ||
| 4-83107861-G-A | not specified | Uncertain significance (Jul 19, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLAC8 | protein_coding | protein_coding | ENST00000426923 | 3 | 47028 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.120 | 0.788 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 46 | 71.2 | 0.646 | 0.00000403 | 753 |
| Missense in Polyphen | 10 | 22.112 | 0.45225 | 286 | ||
| Synonymous | 1.16 | 20 | 27.8 | 0.719 | 0.00000199 | 215 |
| Loss of Function | 1.34 | 2 | 5.33 | 0.375 | 3.12e-7 | 53 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000877 | 0.0000877 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Gastric Cancer Network 2;Differentiation of white and brown adipocyte;Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.385
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.157
- hipred
- N
- hipred_score
- 0.318
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plac8
- Phenotype
- immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- positive regulation of cell population proliferation;response to cold;negative regulation of multicellular organism growth;defense response to bacterium;negative regulation of apoptotic process;neutrophil degranulation;positive regulation of transcription by RNA polymerase II;brown fat cell differentiation;positive regulation of cold-induced thermogenesis
- Cellular component
- extracellular region;azurophil granule lumen
- Molecular function
- chromatin binding