PADI3

peptidyl arginine deiminase 3, the group of Peptidyl arginine deiminases|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:17249097-17284233

Links

ENSG00000142619 ∙ NCBI:51702 ∙ OMIM:606755 ∙ HGNC:18337 ∙ Uniprot:Q9ULW8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• uncombable hair syndrome 1 (Moderate), mode of inheritance: AR
• uncombable hair syndrome 1 (Strong), mode of inheritance: AR
• uncombable hair syndrome (Supportive), mode of inheritance: AR
• uncombable hair syndrome 1 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Uncombable hair syndrome 1	AR	General	The clinical relevance of the condition is unclear	Dermatologic	27866708

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PADI3 gene.

• Inborn genetic diseases (35 variants)
• not provided (8 variants)
• Central centrifugal cicatricial alopecia (6 variants)
• not specified (3 variants)
• Uncombable hair syndrome 1 (2 variants)
• PADI3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PADI3 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				1		1
missense	3	1	37	3		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding						0
Total	4	1	37	4	0

Highest pathogenic variant AF is 0.00238

Variants in PADI3

This is a list of pathogenic ClinVar variants found in the PADI3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-17249134-C-G		PADI3-related disorder	Likely benign (Sep 17, 2019)
1-17249150-A-C		PADI3-related disorder	Benign (Mar 15, 2019)
1-17249156-G-T		Inborn genetic diseases	Uncertain significance (Mar 11, 2024)
1-17249187-C-T		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
1-17249211-C-A		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
1-17259627-G-A		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
1-17259639-A-G		PADI3-related disorder	Benign (Mar 15, 2019)
1-17259663-C-T		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
1-17259699-G-A		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
1-17262154-A-G		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
1-17262169-C-T		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
1-17262194-T-A		Uncombable hair syndrome 1 • PADI3-related disorder	Pathogenic/Likely pathogenic (Mar 26, 2024)
1-17265690-G-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
1-17266737-C-T			Likely benign (Apr 01, 2024)
1-17266752-G-A		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
1-17266814-C-A		Inborn genetic diseases	Uncertain significance (May 30, 2022)
1-17266818-C-T		Inborn genetic diseases	Uncertain significance (Dec 14, 2021)
1-17266821-G-A		PADI3-related disorder	Benign (Mar 15, 2019)
1-17267905-C-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
1-17267907-T-C		PADI3-related disorder	Likely benign (Oct 28, 2019)
1-17267938-C-T		Central centrifugal cicatricial alopecia	Pathogenic (Jul 01, 2018)
1-17267961-C-T		PADI3-related disorder	Likely benign (Jan 02, 2020)
1-17267962-G-A			Uncertain significance (Apr 25, 2023)
1-17270243-T-G		PADI3-related disorder	Benign (May 11, 2020)
1-17270264-T-A		Inborn genetic diseases	Uncertain significance (May 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PADI3	protein_coding	protein_coding	ENST00000375460	16	35136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.36e-10	0.878	125563	0	185	125748	0.000736

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.169	400	410	0.977	0.0000248	4379
Missense in Polyphen		136	143.89	0.9452		1599
Synonymous	0.365	167	173	0.965	0.0000110	1298
Loss of Function	1.81	20	30.8	0.649	0.00000140	354

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00183
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000328	0.000323
European (Non-Finnish)	0.000777	0.000774
Middle Eastern	0.000109	0.000109
South Asian	0.00160	0.00160
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the deimination of arginine residues of proteins. {ECO:0000269|PubMed:27866708}.
• Pathway: Chromatin modifying enzymes;Chromatin organization;protein citrullination (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 1.85
• rvis_percentile_EVS: 97.15

Haploinsufficiency Scores

• pHI: 0.487
• hipred: N
• hipred_score: 0.208

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Padi3
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

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