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ATN1 atrophin 1 [ Homo sapiens (human) ]

Gene ID: 1822, updated on 3-Apr-2024

Summary

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Official Symbol
ATN1provided by HGNC
Official Full Name
atrophin 1provided by HGNC
Primary source
HGNC:HGNC:3033
See related
Ensembl:ENSG00000111676 MIM:607462; AllianceGenome:HGNC:3033
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
B37; HRS; NOD; DRPLA; CHEDDA; D12S755E
Summary
Dentatorubral pallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder characterized by cerebellar ataxia, myoclonic epilepsy, choreoathetosis, and dementia. The disorder is related to the expansion from 7-35 copies to 49-93 copies of a trinucleotide repeat (CAG/CAA) within this gene. The encoded protein includes a serine repeat and a region of alternating acidic and basic amino acids, as well as the variable glutamine repeat. Alternative splicing results in two transcripts variants that encode the same protein. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in ovary (RPKM 68.4), brain (RPKM 46.0) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
12p13.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6924459..6942321)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6935640..6953487)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7033622..7051484)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5890 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:7023548-7023738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7024095-7024736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7024737-7025376 Neighboring gene enolase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5891 Neighboring gene uncharacterized LOC124902868 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7033606-7034306 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7035007-7035706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4194 Neighboring gene atrophin 1 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4195 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:7052993-7053572 and GRCh37_chr12:7053573-7054152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7054402-7055012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7055013-7055621 Neighboring gene chromosome 12 open reading frame 57 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4196 Neighboring gene RNA, U7 small nuclear 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7059817-7060752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7060753-7061686 Neighboring gene protein tyrosine phosphatase non-receptor type 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7061687-7062621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7069919-7070720

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. Atrophin-1 Function and Dysfunction in Dentatorubral-Pallidoluysian Atrophy. Nowak B, et al. Mov Disord, 2023 Apr. PMID 36809552
  2. ATN1-Related Neurodevelopmental Disorder. Adam MP, et al. , 1993. PMID 36007104
  3. CHEDDA syndrome is an underrecognized neurodevelopmental disorder with a highly restricted ATN1 mutation spectrum. Palmer EE, et al. Clin Genet, 2021 Oct. PMID 34212383
  4. De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome. Palmer EE, et al. Am J Hum Genet, 2019 Mar 7. PMID 30827498, Free PMC Article
  5. [Clinical and genetic characteristics of patients with dentatorubro-pallidoluysian atrophy]. Li H, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2016 Oct. PMID 27577205

See all (106) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Atrophin-1 Function and Dysfunction in Dentatorubral-Pallidoluysian Atrophy.
    Title: Atrophin-1 Function and Dysfunction in Dentatorubral-Pallidoluysian Atrophy.
  2. CHEDDA syndrome is an underrecognized neurodevelopmental disorder with a highly restricted ATN1 mutation spectrum.
    Title: CHEDDA syndrome is an underrecognized neurodevelopmental disorder with a highly restricted ATN1 mutation spectrum.
  3. De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Non-Progressive Neurocognitive Syndrome.
    Title: De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome.
  4. Data indicate that the size of the expanded CAG repeats od dentatorubral-pallidoluysian atrophy protein (DRPLA) was inversely correlated with the age at onset.
    Title: [Clinical and genetic characteristics of patients with dentatorubro-pallidoluysian atrophy].
  5. Epigenetic regulation of ATN1 by LSD1 is required for cortical progenitor maintenance.
    Title: Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance.
  6. Juvenile myoclonic epilepsy is not associated with the DRPLA gene in a European population.
    Title: Juvenile myoclonic epilepsy is not associated with the DRPLA gene in a European population.
  7. These data demonstrate that the expanded trinucleotide repeat within ATN-1 mRNA is a potential target for compounds designed to achieve allele-selective inhibition of ATN-1 protein, and one agent may allow the targeting of multiple disease genes.
    Title: Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs.
  8. results suggest that expanded polyQ repeats in ATN1 may contribute to neurodegeneration via alterations in both protein aggregation and intracellular localization.
    Title: Increased aggregation of polyleucine compared with that of polyglutamine in dentatorubral-pallidoluysian atrophy protein.
  9. This study demonistrated that hypoalbuminemia in early onset DRPLA revealed the possibility of multiorgan involvement.
    Title: Hypoalbuminemia in early onset dentatorubral-pallidoluysian atrophy due to leakage of albumin in multiple organs.
  10. In cerebrum and cerebellum of DRPLA transgenic mouse lines at 4, 8, and 12 weeks it is demonstrated that both the number and expression levels of the altered genes are highly dependent on CAG repeat length and age in both brain regions.
    Title: DRPLA transgenic mouse substrains carrying single copy of full-length mutant human DRPLA gene with variable sizes of expanded CAG repeats exhibit CAG repeat length- and age-dependent changes in behavioral abnormalities and gene expression profiles.
Submit: New GeneRIF Correction See all GeneRIFs (30)

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

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

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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell killing IEA
Inferred from Electronic Annotation
more info
  
involved_in cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in determination of adult lifespan IEA
Inferred from Electronic Annotation
more info
  
involved_in maintenance of cell polarity IEA
Inferred from Electronic Annotation
more info
  
involved_in male gonad development IEA
Inferred from Electronic Annotation
more info
  
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neuron apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in response to food IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm TAS
Traceable Author Statement
more info
 PubMed 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
atrophin-1
Names
dentatorubral-pallidoluysian atrophy protein

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_008047.2 RefSeqGene

    Range
    8502..22864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001007026.2 → NP_001007027.1  atrophin-1

    See identical proteins and their annotated locations for NP_001007027.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC051795, BQ448220, BQ880124, BQ897715, U47924
    Consensus CDS
    CCDS31734.1
    UniProtKB/Swiss-Prot
    P54259, Q99495, Q99621, Q9UEK7
    UniProtKB/TrEMBL
    Q86V38
    Related
    ENSP00000349076.3, ENST00000356654.8
    Conserved Domains (1) summary
    pfam03154
    Location:1 → 1189
    Atrophin-1; Atrophin-1 family

  2. NM_001424176.1 → NP_001411105.1  atrophin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    U47924
    UniProtKB/Swiss-Prot
    P54259, Q99495, Q99621, Q9UEK7

  3. NM_001424177.1 → NP_001411106.1  atrophin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    U47924
    UniProtKB/Swiss-Prot
    P54259, Q99495, Q99621, Q9UEK7

  4. NM_001424178.1 → NP_001411107.1  atrophin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    U47924
    UniProtKB/Swiss-Prot
    P54259, Q99495, Q99621, Q9UEK7

  5. NM_001424179.1 → NP_001411108.1  atrophin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    U47924

  6. NM_001424180.1 → NP_001411109.1  atrophin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    U47924

  7. NM_001424181.1 → NP_001411110.1  atrophin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    CP068266

  8. NM_001424182.1 → NP_001411111.1  atrophin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    CP068266

  9. NM_001940.4 → NP_001931.2  atrophin-1

    See identical proteins and their annotated locations for NP_001931.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AW411230, BE142829, BQ448220, BQ897715, BQ957462, D31840, U47924
    Consensus CDS
    CCDS31734.1
    UniProtKB/Swiss-Prot
    P54259, Q99495, Q99621, Q9UEK7
    UniProtKB/TrEMBL
    Q86V38
    Related
    ENSP00000379915.2, ENST00000396684.3
    Conserved Domains (1) summary
    pfam03154
    Location:1 → 1189
    Atrophin-1; Atrophin-1 family

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6924459..6942321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6935640..6953487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P54259.3 GenPept UniProtKB/Swiss-Prot:P54259

Gene LinkOut

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

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