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

Summary

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: mouse all
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Genomic context

Location:: 1p36.13

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (17372196..17401699)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (17186145..17215646)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (17698691..17728195)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Crystal structure of human peptidylarginine deiminase type VI (PAD6) provides insights into its inactivity.
Title: Crystal structure of human peptidylarginine deiminase type VI (PAD6) provides insights into its inactivity.
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.
Novel biallelic mutations in PADI6 in patients with early embryonic arrest.
Title: Novel biallelic mutations in PADI6 in patients with early embryonic arrest.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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	Compare labs

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 EBI GWAS CatalogPubMed
Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL009774 (e-PCR)
- UniSTS:54567

D1S2601 (e-PCR)
- UniSTS:74616

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
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
NOT contributes_to protein-arginine deiminase activity	IDA Inferred from Direct Assay more info	PubMed

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

EC 3.5.3.15

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

NG_032943.2 RefSeqGene

Range

4951..34454

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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