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PADI6 peptidyl arginine deiminase 6 [ Homo sapiens (human) ]

Gene ID: 353238, updated on 5-Mar-2024

Summary

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Official Symbol
PADI6provided by HGNC
Official Full Name
peptidyl arginine deiminase 6provided by HGNC
Primary source
HGNC:HGNC:20449
See related
Ensembl:ENSG00000276747 MIM:610363; AllianceGenome:HGNC:20449
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
hPADVI; OZEMA16; PREMBL2
Summary
This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. This protein may play a role in cytoskeletal reorganization in the egg and in early embryo development. [provided by RefSeq, Sep 2012]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
1p36.13
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (17372196..17401699)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (17186145..17215646)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (17698691..17728195)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene peptidyl arginine deiminase 3 Neighboring gene microRNA 3972 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:17621951-17622120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17631014-17631874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17642404-17642961 Neighboring gene peptidyl arginine deiminase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17685053-17685772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17703685-17704186 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:17707761-17708960 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:17720217-17721416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17727331-17728267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17743473-17744343 Neighboring gene RCC2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:17746283-17746817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17748547-17749301 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:17752063-17752701 Neighboring gene regulator of chromosome condensation 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:17754621-17755259 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:17755305-17755919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 343 Neighboring gene uncharacterized LOC124903862

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Novel biallelic mutations in PADI6 in patients with early embryonic arrest. Dong J, et al. J Hum Genet, 2022 May. PMID 34987164
  2. Biallelic PADI6 variants cause multilocus imprinting disturbances and miscarriages in the same family. Eggermann T, et al. Eur J Hum Genet, 2021 Apr. PMID 33221824, Free PMC Article
  3. Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance. Cubellis MV, et al. Clin Epigenetics, 2020 Sep 14. PMID 32928291, Free PMC Article
  4. New biallelic mutations in PADI6 cause recurrent preimplantation embryonic arrest characterized by direct cleavage. Zheng W, et al. J Assist Reprod Genet, 2020 Jan. PMID 31664658, Free PMC Article
  5. The human knockout phenotype of PADI6 is female sterility caused by cleavage failure of their fertilized eggs. Maddirevula S, et al. Clin Genet, 2017 Feb. PMID 27730629

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Case report: human early embryonic arrest in a consanguineous Chinese family caused by a novel missense variant of PADI6.
    Title: Case report: human early embryonic arrest in a consanguineous Chinese family caused by a novel missense variant of PADI6.
  2. Novel biallelic mutations in PADI6 in patients with early embryonic arrest.
    Title: Novel biallelic mutations in PADI6 in patients with early embryonic arrest.
  3. Genetic Variation in PADI6-PADI4 on 1p36.13 Is Associated with Common Forms of Human Generalized Epilepsy.
    Title: Genetic Variation in PADI6-PADI4 on 1p36.13 Is Associated with Common Forms of Human Generalized Epilepsy.
  4. Novel pathogenic variants in NLRP7, NLRP5, and PADI6 in patients with recurrent hydatidiform moles and reproductive failure.
    Title: Novel pathogenic variants in NLRP7, NLRP5, and PADI6 in patients with recurrent hydatidiform moles and reproductive failure.
  5. Biallelic PADI6 variants cause multilocus imprinting disturbances and miscarriages in the same family.
    Title: Biallelic PADI6 variants cause multilocus imprinting disturbances and miscarriages in the same family.
  6. Two novel mutations in PADI6 and TLE6 genes cause female infertility due to arrest in embryonic development.
    Title: Two novel mutations in PADI6 and TLE6 genes cause female infertility due to arrest in embryonic development.
  7. Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance.
    Title: Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance.
  8. New biallelic mutations in PADI6 cause recurrent preimplantation embryonic arrest characterized by direct cleavage.
    Title: New biallelic mutations in PADI6 cause recurrent preimplantation embryonic arrest characterized by direct cleavage.
  9. We now report 15 further pedigrees in which offspring had disturbance of imprinting, while their mothers had rare, predicted-deleterious variants in maternal effect genes, including NLRP2, NLRP7 and PADI6
    Title: Maternal variants in NLRP and other maternal effect proteins are associated with multilocus imprinting disturbance in offspring.
  10. We demonstrated that PADI6 co-localizes with NLRP7 in human oocytes and preimplantation embryos and reviewed the morphology and genotypes of four products of conception from our patient
    Title: Biallelic PADI6 variants linking infertility, miscarriages, and hydatidiform moles.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Preimplantation embryonic lethality 2
MedGen: C4310659 OMIM: 617234 GeneReviews: Not available
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EBI GWAS Catalog

Description
Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits.
EBI GWAS Catalog
Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-arginine deiminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cytoplasm organization IEA
Inferred from Electronic Annotation
more info
  
involved_in cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic cleavage ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of translation by machinery localization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cortical granule ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in intermediate filament cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein-arginine deiminase type-6
Names
peptidyl arginine deiminase, type VI
peptidyl arginine deiminase-like protein
peptidylarginine deiminase type 6
NP_997304.3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032943.2 RefSeqGene

    Range
    4951..34454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_207421.4 → NP_997304.3  protein-arginine deiminase type-6

    See identical proteins and their annotated locations for NP_997304.3

    Status: REVIEWED

    Source sequence(s)
    AY422079, AY443100
    Consensus CDS
    CCDS72715.1
    UniProtKB/Swiss-Prot
    Q330K5, Q6TGC4, Q70SX3
    Related
    ENSP00000483125.1, ENST00000619609.1
    Conserved Domains (3) summary
    pfam03068
    Location:295 → 691
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:9 → 120
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:122 → 280
    PAD_M; Protein-arginine deiminase (PAD) middle domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    17372196..17401699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332688.1 Reference GRCh38.p14 PATCHES

    Range
    217419..246922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    17186145..17215646
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6TGC4.3 GenPept UniProtKB/Swiss-Prot:Q6TGC4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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