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.

• 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		21
missense	1	6	30	5	1	43
nonsense		1				1
start loss						0
frameshift	6	2	1			9
inframe indel						0
splice donor/acceptor (+/-2bp)				2		2
splice region			1	2		3
non coding				4	1	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)
1-17372308-C-G		Inborn genetic diseases	Uncertain significance (May 10, 2024)
1-17373074-C-T		PADI6-related disorder	Likely benign (Jul 25, 2022)
1-17373091-A-G		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
1-17373127-C-T		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
1-17373181-C-T		Inborn genetic diseases	Likely benign (Jun 24, 2022)
1-17373182-G-A		PADI6-related disorder	Likely benign (Mar 01, 2023)
1-17373185-C-T		PADI6-related disorder	Likely benign (Nov 22, 2021)
1-17373188-C-T		PADI6-related disorder	Likely benign (Mar 30, 2020)
1-17373203-A-G		PADI6-related disorder	Likely benign (Oct 27, 2020)
1-17373205-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
1-17373219-G-A			Uncertain significance (Jul 01, 2022)
1-17373219-G-T		Inborn genetic diseases	Uncertain significance (Feb 01, 2022)
1-17373225-G-A		PADI6-related disorder	Likely benign (Jan 10, 2024)
1-17373238-G-A		Preimplantation embryonic lethality 2	Uncertain significance (Nov 01, 2021)
1-17375449-C-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
1-17375466-G-A		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
1-17379905-TTTC-T		PADI6-related disorder	Likely benign (Mar 25, 2021)
1-17379933-G-T		Inborn genetic diseases	Likely benign (Apr 25, 2022)
1-17379947-G-A		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
1-17381046-G-GA		PADI6-related disorder	Likely pathogenic (Jun 06, 2023)
1-17381130-G-C		Premature ovarian failure	Uncertain significance (Apr 22, 2019)
1-17381152-A-T		Inborn genetic diseases	Likely benign (Apr 25, 2022)
1-17381970-T-TA		Preimplantation embryonic lethality 2	Pathogenic (Nov 01, 2021)
1-17382009-C-G		Inborn genetic diseases	Uncertain significance (May 09, 2024)

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

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