PADI6

peptidyl arginine deiminase 6, the group of Peptidyl arginine deiminases

Basic information

Region (hg38): 1:17372196-17401699

Links

ENSG00000276747NCBI:353238OMIM:610363HGNC:20449Uniprot:Q6TGC4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Oocyte/zygote/embryo maturation arrest 16ARObstetricGenetic knowledge may be beneficial to allow reproductive-related interventionsObstetric27545678

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.

EffectPLPVUSLBBSum
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