PLRG1
Basic information
Region (hg38): 4:154535005-154550400
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLRG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002669.4. 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 | 1 | |||||
| missense | 39 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 39 | 2 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLRG1 | protein_coding | protein_coding | ENST00000499023 | 15 | 15430 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000895 | 125690 | 0 | 4 | 125694 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 167 | 283 | 0.590 | 0.0000144 | 3357 |
| Missense in Polyphen | 48 | 135.06 | 0.35539 | 1603 | ||
| Synonymous | 1.73 | 76 | 97.8 | 0.777 | 0.00000522 | 968 |
| Loss of Function | 4.89 | 3 | 33.5 | 0.0894 | 0.00000186 | 371 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000617 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000272 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:28502770, PubMed:28076346). Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing (PubMed:11101529, PubMed:11544257). {ECO:0000269|PubMed:11101529, ECO:0000269|PubMed:11544257, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.;
- Pathway
- Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.153
Intolerance Scores
- loftool
- 0.346
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 33.2
Haploinsufficiency Scores
- pHI
- 0.555
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.646
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.497
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plrg1
- Phenotype
- cellular phenotype; muscle 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); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- plrg1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- truncated
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;protein localization to nucleus;positive regulation of G1/S transition of mitotic cell cycle
- Cellular component
- Prp19 complex;fibrillar center;nucleus;nucleoplasm;DNA replication factor A complex;nuclear speck;nuclear membrane;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;Cul4-RING E3 ubiquitin ligase complex
- Molecular function
- protein binding