PAPOLG
Basic information
Region (hg38): 2:60756253-60802086
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 PAPOLG 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 | 23 | 23 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 23 | 1 | 1 |
Variants in PAPOLG
This is a list of pathogenic ClinVar variants found in the PAPOLG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-60761755-G-A | not specified | Uncertain significance (Apr 14, 2022) | ||
2-60768829-C-G | not specified | Uncertain significance (Mar 30, 2024) | ||
2-60768883-A-G | not specified | Uncertain significance (Jan 30, 2024) | ||
2-60771544-C-G | not specified | Uncertain significance (Sep 23, 2023) | ||
2-60771630-G-A | Uncertain significance (Jun 29, 2023) | |||
2-60780778-G-A | not specified | Uncertain significance (Nov 30, 2022) | ||
2-60781918-A-G | not specified | Uncertain significance (Sep 20, 2023) | ||
2-60782678-TAA-T | Benign (Nov 14, 2017) | |||
2-60782680-A-ATTTTTTTTTTTTTT | Benign (Nov 14, 2017) | |||
2-60782680-A-ATTTTTTTTTTTTTTTTTTTTTTT | Likely benign (Aug 18, 2017) | |||
2-60782734-A-G | not specified | Uncertain significance (Jan 08, 2024) | ||
2-60787057-A-G | not specified | Uncertain significance (Nov 23, 2021) | ||
2-60787527-A-G | not specified | Uncertain significance (Oct 27, 2021) | ||
2-60791823-G-A | not specified | Uncertain significance (Aug 19, 2023) | ||
2-60791830-A-C | not specified | Uncertain significance (May 13, 2024) | ||
2-60791879-A-T | not specified | Uncertain significance (Mar 15, 2024) | ||
2-60792162-G-A | not specified | Uncertain significance (Feb 02, 2022) | ||
2-60792247-C-T | not specified | Uncertain significance (Oct 16, 2023) | ||
2-60792277-G-T | not specified | Uncertain significance (Nov 03, 2023) | ||
2-60793628-A-G | not specified | Uncertain significance (Jan 30, 2024) | ||
2-60793973-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
2-60793992-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
2-60794000-C-T | not specified | Uncertain significance (Nov 14, 2023) | ||
2-60794030-G-C | not specified | Uncertain significance (Dec 14, 2021) | ||
2-60794054-A-G | not specified | Uncertain significance (Jun 16, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PAPOLG | protein_coding | protein_coding | ENST00000238714 | 22 | 45856 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.998 | 0.00210 | 125726 | 0 | 18 | 125744 | 0.0000716 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.20 | 271 | 394 | 0.688 | 0.0000205 | 4793 |
Missense in Polyphen | 28 | 101.07 | 0.27703 | 1302 | ||
Synonymous | 0.993 | 120 | 135 | 0.891 | 0.00000685 | 1420 |
Loss of Function | 5.35 | 6 | 44.5 | 0.135 | 0.00000239 | 527 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000188 | 0.000185 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000895 | 0.0000879 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000983 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Responsible for the post-transcriptional adenylation of the 3'-terminal of mRNA precursors and several small RNAs including signal recognition particle (SRP) RNA, nuclear 7SK RNA, U2 small nuclear RNA, and ribosomal 5S RNA. {ECO:0000269|PubMed:11287430, ECO:0000269|PubMed:11463842}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);Purine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.135
- rvis_EVS
- -0.87
- rvis_percentile_EVS
- 10.73
Haploinsufficiency Scores
- pHI
- 0.432
- hipred
- Y
- hipred_score
- 0.527
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.695
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Papolg
- Phenotype
Gene ontology
- Biological process
- mRNA polyadenylation;RNA polyadenylation
- Cellular component
- nucleus;nucleoplasm;cytosol;membrane;nuclear body
- Molecular function
- RNA binding;polynucleotide adenylyltransferase activity;ATP binding;metal ion binding