PADI2

peptidyl arginine deiminase 2, the group of Peptidyl arginine deiminases

Basic information

Region (hg38): 1:17066761-17119451

Links

ENSG00000117115

∙ NCBI:11240 ∙ OMIM:607935 ∙ HGNC:18341 ∙ Uniprot:Q9Y2J8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (86 variants)
not_provided (7 variants)

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. These statistics are base on transcript: NM_000007365.3. 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					5 clinvar	5
missense			84 clinvar	3 clinvar		87
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	4	5

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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