PADI6
Basic information
Region (hg38): 1:17372196-17401699
Links
Phenotypes
GenCC
Source:
- preimplantation embryonic lethality 2 (Strong), mode of inheritance: AR
- preimplantation embryonic lethality 2 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
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
- 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 | 22 | ||||
missense | 60 | 77 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 10 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
Total | 9 | 12 | 62 | 32 | 1 |
Highest pathogenic variant AF is 0.00006011
GnomAD
Source:
dbNSFP
Source:
- 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