PADI2

peptidyl arginine deiminase 2, the group of Peptidyl arginine deiminases

Basic information

Region (hg38): 1:17066761-17119451

Links

ENSG00000117115NCBI:11240OMIM:607935HGNC:18341Uniprot:Q9Y2J8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PADI2 gene.

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
clinvar
5
missense
36
clinvar
2
clinvar
38
nonsense
1
clinvar
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)972888
1-17069087-C-T not specified Uncertain significance (May 30, 2024)3303904
1-17069100-C-T not specified Uncertain significance (Sep 14, 2022)2403249
1-17069161-G-A Benign (Mar 29, 2018)783278
1-17069170-G-A Benign (Jun 18, 2018)729657
1-17069187-G-A not specified Uncertain significance (Aug 13, 2021)3207946
1-17069190-C-T not specified Uncertain significance (Nov 22, 2023)3207945
1-17069250-G-C not specified Uncertain significance (Mar 28, 2023)2530738
1-17070118-G-T not specified Uncertain significance (Sep 14, 2022)2311913
1-17070122-T-G not specified Uncertain significance (Mar 24, 2023)2525523
1-17070123-C-T not specified Likely benign (Mar 30, 2024)3303905
1-17070197-C-T not specified Uncertain significance (Aug 15, 2023)2597958
1-17071438-C-T not specified Uncertain significance (Jan 26, 2022)2401575
1-17071462-T-A not specified Uncertain significance (May 18, 2023)2548640
1-17074863-C-A not specified Uncertain significance (Apr 13, 2023)2536700
1-17074863-C-T not specified Uncertain significance (Dec 16, 2023)3207944
1-17074942-A-C not specified Likely benign (Jan 24, 2023)2463257
1-17075687-C-T not specified Uncertain significance (Jan 16, 2024)3207943
1-17075721-G-A Benign (Dec 31, 2019)773390
1-17075797-A-G not specified Uncertain significance (Oct 04, 2024)3413234
1-17075812-C-T not specified Uncertain significance (Aug 05, 2024)3413233
1-17075813-G-A not specified Uncertain significance (Mar 26, 2024)3303908
1-17079288-A-G not specified Uncertain significance (Apr 29, 2024)3303910
1-17079300-G-A not specified Uncertain significance (Oct 20, 2024)3413228
1-17079342-A-G not specified Uncertain significance (Aug 14, 2023)2617951

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PADI2protein_codingprotein_codingENST00000375486 1652693
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.95e-110.94412521105361257470.00213
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4903854130.9320.00002564346
Missense in Polyphen144167.250.861011792
Synonymous0.1671721750.9840.00001191295
Loss of Function2.072235.30.6240.00000193386

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002670.00265
Ashkenazi Jewish0.001120.00109
East Asian0.0002720.000272
Finnish0.001340.00134
European (Non-Finnish)0.003130.00313
Middle Eastern0.0002720.000272
South Asian0.002190.00219
Other0.0009790.000978

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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