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.

  • Preimplantation embryonic lethality 2 (7 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.

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
21
clinvar
21
missense
1
clinvar
6
clinvar
30
clinvar
5
clinvar
1
clinvar
43
nonsense
1
clinvar
1
start loss
0
frameshift
6
clinvar
2
clinvar
1
clinvar
9
inframe indel
0
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
1
2
3
non coding
4
clinvar
1
clinvar
5
Total 7 9 31 32 2

Variants in PADI6

This is a list of pathogenic ClinVar variants found in the PADI6 region.

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

Position Type Phenotype Significance ClinVar
1-17372249-G-GT Preimplantation embryonic lethality 2 Pathogenic (Nov 01, 2021)1308687
1-17372308-C-G Inborn genetic diseases Uncertain significance (May 10, 2024)3303927
1-17373074-C-T PADI6-related disorder Likely benign (Jul 25, 2022)3031452
1-17373091-A-G Inborn genetic diseases Uncertain significance (Aug 12, 2021)2243462
1-17373127-C-T Inborn genetic diseases Uncertain significance (Feb 05, 2024)3207982
1-17373181-C-T Inborn genetic diseases Likely benign (Jun 24, 2022)2342929
1-17373182-G-A PADI6-related disorder Likely benign (Mar 01, 2023)1334958
1-17373185-C-T PADI6-related disorder Likely benign (Nov 22, 2021)3054182
1-17373188-C-T PADI6-related disorder Likely benign (Mar 30, 2020)3054892
1-17373203-A-G PADI6-related disorder Likely benign (Oct 27, 2020)3033044
1-17373205-C-T Inborn genetic diseases Uncertain significance (Dec 21, 2022)2211713
1-17373219-G-A Uncertain significance (Jul 01, 2022)1701095
1-17373219-G-T Inborn genetic diseases Uncertain significance (Feb 01, 2022)1675348
1-17373225-G-A PADI6-related disorder Conflicting classifications of pathogenicity (Aug 01, 2023)1176184
1-17373238-G-A Preimplantation embryonic lethality 2 Uncertain significance (Nov 01, 2021)1308685
1-17375449-C-A Inborn genetic diseases Uncertain significance (Aug 02, 2022)2209894
1-17375466-G-A Inborn genetic diseases Uncertain significance (Jun 02, 2023)2561525
1-17379905-TTTC-T PADI6-related disorder Likely benign (Mar 25, 2021)3054348
1-17379933-G-T Inborn genetic diseases Likely benign (Apr 25, 2022)2285327
1-17379947-G-A Inborn genetic diseases Uncertain significance (Sep 22, 2023)3207983
1-17381046-G-GA PADI6-related disorder Likely pathogenic (May 29, 2024)2633287
1-17381130-G-C Premature ovarian failure Uncertain significance (Apr 22, 2019)812130
1-17381152-A-T Inborn genetic diseases Likely benign (Apr 25, 2022)2269430
1-17381970-T-TA Preimplantation embryonic lethality 2 Pathogenic (Nov 01, 2021)1308678
1-17382009-C-G Inborn genetic diseases Uncertain significance (May 09, 2024)3303930

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