POP7
Basic information
Region (hg38): 7:100706121-100707486
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 POP7 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 | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 0 |
Variants in POP7
This is a list of pathogenic ClinVar variants found in the POP7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-100706852-C-T | not specified | Uncertain significance (May 20, 2024) | ||
| 7-100706853-G-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 7-100706898-G-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 7-100706904-G-A | not specified | Uncertain significance (May 07, 2024) | ||
| 7-100706915-C-T | not specified | Uncertain significance (Oct 06, 2022) | ||
| 7-100707000-A-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 7-100707009-C-A | not specified | Uncertain significance (Dec 11, 2023) | ||
| 7-100707024-C-A | not specified | Uncertain significance (Nov 26, 2024) | ||
| 7-100707035-A-G | not specified | Uncertain significance (Nov 13, 2024) | ||
| 7-100707081-T-C | not specified | Uncertain significance (Aug 20, 2023) | ||
| 7-100707121-G-C | not specified | Uncertain significance (Oct 04, 2024) | ||
| 7-100707128-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 7-100707132-A-G | not specified | Uncertain significance (Jul 15, 2021) | ||
| 7-100707156-A-C | not specified | Uncertain significance (Oct 06, 2022) | ||
| 7-100707179-A-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 7-100707182-C-T | not specified | Uncertain significance (Aug 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POP7 | protein_coding | protein_coding | ENST00000303151 | 1 | 1443 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0375 | 0.653 | 125729 | 0 | 7 | 125736 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.457 | 74 | 85.9 | 0.861 | 0.00000523 | 891 |
| Missense in Polyphen | 15 | 23.655 | 0.63412 | 263 | ||
| Synonymous | -0.0883 | 39 | 38.3 | 1.02 | 0.00000242 | 316 |
| Loss of Function | 0.408 | 2 | 2.73 | 0.733 | 1.22e-7 | 34 |
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) | 0.0000440 | 0.0000440 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP complex, which cleaves pre-rRNA sequences.;
- Pathway
- Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Metabolism of RNA;tRNA processing in the nucleus
(Consensus)
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- loftool
- 0.283
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.11
Haploinsufficiency Scores
- pHI
- 0.0887
- hipred
- Y
- hipred_score
- 0.614
- ghis
- 0.545
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pop7
- Phenotype
Gene ontology
- Biological process
- tRNA 5'-leader removal;tRNA processing;RNA phosphodiester bond hydrolysis, endonucleolytic
- Cellular component
- ribonuclease MRP complex;nucleus;nucleoplasm;nucleolar ribonuclease P complex;cytoplasm;multimeric ribonuclease P complex
- Molecular function
- RNA binding;ribonuclease P activity;protein binding