PADI3

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

Basic information

Region (hg38): 1:17249098-17284233

Links

ENSG00000142619NCBI:51702OMIM:606755HGNC:18337Uniprot:Q9ULW8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
  • uncombable hair syndrome 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Uncombable hair syndrome 1ARGeneralThe clinical relevance of the condition is unclearDermatologic27866708

ClinVar

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

  • Inborn_genetic_diseases (105 variants)
  • PADI3-related_disorder (12 variants)
  • not_provided (10 variants)
  • Central_centrifugal_cicatricial_alopecia (6 variants)
  • Uncombable_hair_syndrome_1 (6 variants)
  • not_specified (2 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. These statistics are base on transcript: NM_000016233.2. 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
1
clinvar
6
missense
4
clinvar
4
clinvar
104
clinvar
6
clinvar
1
clinvar
119
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total 6 5 104 11 2

Highest pathogenic variant AF is 0.00756088

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PADI3protein_codingprotein_codingENST00000375460 1635136
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.36e-100.87812556301851257480.000736
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1694004100.9770.00002484379
Missense in Polyphen136143.890.94521599
Synonymous0.3651671730.9650.00001101298
Loss of Function1.812030.80.6490.00000140354

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001830.00183
Ashkenazi Jewish0.00009940.0000992
East Asian0.0001090.000109
Finnish0.0003280.000323
European (Non-Finnish)0.0007770.000774
Middle Eastern0.0001090.000109
South Asian0.001600.00160
Other0.0006550.000652

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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