PADI1

peptidyl arginine deiminase 1, the group of Peptidyl arginine deiminases

Basic information

Region (hg38): 1:17205128-17246007

Links

ENSG00000142623 ∙ NCBI:29943 ∙ OMIM:607934 ∙ HGNC:18367 ∙ Uniprot:Q9ULC6 ∙ 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 PADI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PADI1 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			44	2	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	44	2	1

Variants in PADI1

This is a list of pathogenic ClinVar variants found in the PADI1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-17205231-G-T		not specified	Uncertain significance (Oct 08, 2024)
1-17222320-G-T		not specified	Uncertain significance (Dec 03, 2024)
1-17222336-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-17222378-G-A		not specified	Uncertain significance (Jun 16, 2023)
1-17222384-A-G		not specified	Uncertain significance (Jan 20, 2023)
1-17222396-C-T		not specified	Uncertain significance (Jun 10, 2024)
1-17222403-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-17223627-G-T		not specified	Uncertain significance (Jul 12, 2022)
1-17223666-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-17223667-G-A		not specified	Likely benign (Mar 26, 2024)
1-17223681-C-G		not specified	Uncertain significance (Oct 09, 2024)
1-17223690-G-A		not specified	Uncertain significance (Jan 07, 2022)
1-17224367-A-G		not specified	Uncertain significance (Oct 05, 2022)
1-17225853-C-A		not specified	Uncertain significance (Dec 16, 2022)
1-17225868-C-T		not specified	Uncertain significance (Jun 22, 2023)
1-17226065-T-G		not specified	Uncertain significance (Jan 31, 2023)
1-17226066-G-T		not specified	Uncertain significance (Aug 26, 2024)
1-17226075-C-T		not specified	Uncertain significance (Dec 03, 2024)
1-17226078-A-G			Likely benign (May 15, 2018)
1-17226089-G-T		not specified	Uncertain significance (Jan 18, 2023)
1-17226099-A-G		not specified	Uncertain significance (Nov 10, 2021)
1-17226149-T-C		not specified	Uncertain significance (Aug 19, 2024)
1-17226156-G-T		not specified	Uncertain significance (Aug 25, 2024)
1-17228736-C-T		not specified	Uncertain significance (Dec 02, 2024)
1-17228740-C-A		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PADI1	protein_coding	protein_coding	ENST00000375471	16	40880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.04e-15	0.105	125197	1	550	125748	0.00219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	446	388	1.15	0.0000222	4345
Missense in Polyphen		205	183.5	1.1172		2047
Synonymous	-1.56	185	160	1.16	0.00000962	1285
Loss of Function	0.948	26	31.8	0.818	0.00000151	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00229	0.00229
Ashkenazi Jewish	0.00278	0.00278
East Asian	0.00228	0.00229
Finnish	0.00643	0.00640
European (Non-Finnish)	0.00219	0.00218
Middle Eastern	0.00228	0.00229
South Asian	0.000589	0.000588
Other	0.00277	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the deimination of arginine residues of proteins. {ECO:0000269|PubMed:12416996, ECO:0000269|PubMed:27393304}.
• Pathway: Chromatin modifying enzymes;Chromatin organization;protein citrullination (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.875
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.69

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.208
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.488

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Padi1

Gene ontology

• Biological process: protein citrullination;histone citrullination
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: protein-arginine deiminase activity;calcium ion binding