PADI2
Basic information
Region (hg38): 1:17066761-17119451
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 PADI2 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 | 5 | |||||
missense | 36 | 38 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 36 | 3 | 5 |
Variants in PADI2
This is a list of pathogenic ClinVar variants found in the PADI2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-17068786-T-A | Rheumatoid arthritis;Abnormal pulmonary interstitial morphology | association (Feb 01, 2020) | ||
1-17069087-C-T | not specified | Uncertain significance (May 30, 2024) | ||
1-17069100-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
1-17069161-G-A | Benign (Mar 29, 2018) | |||
1-17069170-G-A | Benign (Jun 18, 2018) | |||
1-17069187-G-A | not specified | Uncertain significance (Aug 13, 2021) | ||
1-17069190-C-T | not specified | Uncertain significance (Nov 22, 2023) | ||
1-17069250-G-C | not specified | Uncertain significance (Mar 28, 2023) | ||
1-17070118-G-T | not specified | Uncertain significance (Sep 14, 2022) | ||
1-17070122-T-G | not specified | Uncertain significance (Mar 24, 2023) | ||
1-17070123-C-T | not specified | Likely benign (Mar 30, 2024) | ||
1-17070197-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
1-17071438-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
1-17071462-T-A | not specified | Uncertain significance (May 18, 2023) | ||
1-17074863-C-A | not specified | Uncertain significance (Apr 13, 2023) | ||
1-17074863-C-T | not specified | Uncertain significance (Dec 16, 2023) | ||
1-17074942-A-C | not specified | Likely benign (Jan 24, 2023) | ||
1-17075687-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
1-17075721-G-A | Benign (Dec 31, 2019) | |||
1-17075797-A-G | not specified | Uncertain significance (Oct 04, 2024) | ||
1-17075812-C-T | not specified | Uncertain significance (Aug 05, 2024) | ||
1-17075813-G-A | not specified | Uncertain significance (Mar 26, 2024) | ||
1-17079288-A-G | not specified | Uncertain significance (Apr 29, 2024) | ||
1-17079300-G-A | not specified | Uncertain significance (Oct 20, 2024) | ||
1-17079342-A-G | not specified | Uncertain significance (Aug 14, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PADI2 | protein_coding | protein_coding | ENST00000375486 | 16 | 52693 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.95e-11 | 0.944 | 125211 | 0 | 536 | 125747 | 0.00213 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.490 | 385 | 413 | 0.932 | 0.0000256 | 4346 |
Missense in Polyphen | 144 | 167.25 | 0.86101 | 1792 | ||
Synonymous | 0.167 | 172 | 175 | 0.984 | 0.0000119 | 1295 |
Loss of Function | 2.07 | 22 | 35.3 | 0.624 | 0.00000193 | 386 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00267 | 0.00265 |
Ashkenazi Jewish | 0.00112 | 0.00109 |
East Asian | 0.000272 | 0.000272 |
Finnish | 0.00134 | 0.00134 |
European (Non-Finnish) | 0.00313 | 0.00313 |
Middle Eastern | 0.000272 | 0.000272 |
South Asian | 0.00219 | 0.00219 |
Other | 0.000979 | 0.000978 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the deimination of arginine residues of proteins. {ECO:0000269|PubMed:12392711, ECO:0000269|PubMed:25621824}.;
- Pathway
- Neutrophil degranulation;Chromatin modifying enzymes;Innate Immune System;Immune System;Chromatin organization;protein citrullination
(Consensus)
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.800
- rvis_EVS
- -0.5
- rvis_percentile_EVS
- 21.81
Haploinsufficiency Scores
- pHI
- 0.124
- hipred
- N
- hipred_score
- 0.431
- ghis
- 0.449
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.260
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Padi2
- Phenotype
- immune 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);
Zebrafish Information Network
- Gene name
- padi2
- Affected structure
- ocular blood vessel
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- regulation of chromatin disassembly;protein citrullination;substantia nigra development;intracellular estrogen receptor signaling pathway;histone H3-R26 citrullination;histone citrullination;neutrophil degranulation;chromatin-mediated maintenance of transcription;negative regulation of chemokine-mediated signaling pathway;negative regulation of lymphocyte chemotaxis;cellular response to leukemia inhibitory factor
- Cellular component
- extracellular region;nucleus;cytoplasm;cytosol;transcriptionally active chromatin;azurophil granule lumen;extracellular exosome
- Molecular function
- protein-arginine deiminase activity;calcium ion binding;estrogen receptor binding;protein homodimerization activity