PADI6

peptidyl arginine deiminase 6, the group of Peptidyl arginine deiminases

Basic information

Region (hg38): 1:17372196-17401699

Links

ENSG00000276747

∙ NCBI:353238 ∙ OMIM:610363 ∙ HGNC:20449 ∙ Uniprot:Q6TGC4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

preimplantation embryonic lethality 2 (Strong), mode of inheritance: AR
preimplantation embryonic lethality 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oocyte/zygote/embryo maturation arrest 16	AR	Obstetric	Genetic knowledge may be beneficial to allow reproductive-related interventions	Obstetric	27545678

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PADI6 gene.

Inborn_genetic_diseases (64 variants)
PADI6-related_disorder (32 variants)
Preimplantation_embryonic_lethality_2 (24 variants)
not_provided (7 variants)
Premature_ovarian_failure (1 variants)
not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PADI6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000207421.4. 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				22 clinvar		22
missense	1 clinvar	6 clinvar	60 clinvar	9 clinvar	1 clinvar	77
nonsense	2 clinvar	2 clinvar				4
start loss						0
frameshift	6 clinvar	3 clinvar	1 clinvar			10
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar	1 clinvar		3
Total	9	12	62	32	1

Highest pathogenic variant AF is 0.00006011

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the deimination of arginine residues of proteins (By similarity). May be involved in cytoskeletal reorganization in the egg and early embryo (PubMed:27545678). {ECO:0000250, ECO:0000269|PubMed:27545678}.;
Disease: DISEASE: Preimplantation embryonic lethality 2 (PREMBL2) [MIM:617234]: A rare cause of female primary infertility. In affected women, ovulation and fertilization proceed normally but embryos are arrested at early stages of development. Inheritance is autosomal recessive. {ECO:0000269|PubMed:27545678}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Preimplantation Embryo;Chromatin modifying enzymes;Chromatin organization;protein citrullination (Consensus)

Recessive Scores

pRec: 0.100

Haploinsufficiency Scores

pHI: 0.0656
hipred
hipred_score
ghis

Mouse Genome Informatics

Gene name: Padi6
Phenotype: embryo phenotype; reproductive system phenotype;

Gene ontology

Biological process: cytoskeleton organization;cytoplasm organization;histone citrullination;regulation of translation by machinery localization
Cellular component: nucleus;cytoplasm;intermediate filament cytoskeleton
Molecular function: protein-arginine deiminase activity;calcium ion binding