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    ARMC9 armadillo repeat containing 9 [ Homo sapiens (human) ]

    Gene ID: 80210, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ARMC9provided by HGNC
    Official Full Name
    armadillo repeat containing 9provided by HGNC
    Primary source
    HGNC:HGNC:20730
    See related
    Ensembl:ENSG00000135931 MIM:617612; AllianceGenome:HGNC:20730
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ARM; NS21; JBTS30; KU-MEL-1
    Summary
    Predicted to be involved in cilium assembly and positive regulation of smoothened signaling pathway. Located in centriole and ciliary basal body. Implicated in Joubert syndrome 30. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in endometrium (RPKM 2.3), ovary (RPKM 1.9) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARMC9 in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (231198631..231376848)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231683119..231861312)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (232063345..232241559)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, non-ATPase 1 Neighboring gene 5-hydroxytryptamine receptor 2B Neighboring gene RNA, U1 small nuclear 93, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17276 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:232046423-232047622 Neighboring gene Sharpr-MPRA regulatory region 12701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232056223-232057103 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232111208-232111926 Neighboring gene ribosomal protein S28 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17280 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232181499-232182000 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232182001-232182500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232196977-232197934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232201084-232201584 Neighboring gene Sharpr-MPRA regulatory region 9410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232233755-232234401 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232234402-232235049 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232235050-232235696 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232235697-232236344 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:232240900-232241463 Neighboring gene microRNA 4777 Neighboring gene Sharpr-MPRA regulatory region 14998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232256876-232257459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232258043-232258625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232258626-232259207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12425 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:232261821-232263020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232263273-232263820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232263821-232264366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232266008-232266553 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:232275119-232275724 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:232275725-232276329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12426 Neighboring gene uncharacterized LOC124907997 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:232278424-232279184 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Association Study of ARMC9 Gene Variants with Vogt-Koyanagi-Harada Disease in Japanese Patients. Ohno T, et al. Ocul Immunol Inflamm, 2019. PMID 30395750
    2. Whole exome sequencing reveals a mutation in ARMC9 as a cause of mental retardation, ptosis, and polydactyly. Kar A, et al. Am J Med Genet A, 2018 Jan. PMID 29159890
    3. Tumor antigens isolated from a patient with vitiligo and T-cell-infiltrated melanoma. Kiniwa Y, et al. Cancer Res, 2001 Nov 1. PMID 11691810
    4. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. Van De Weghe JC, et al. Am J Hum Genet, 2017 Jul 6. PMID 28625504, Free PMC Article
    5. Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome. Latour BL, et al. J Clin Invest, 2020 Aug 3. PMID 32453716, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our study suggests that ARMC9 variants do not play a critical role in the development of Vogt-Koyanagi disease.
      Title: Association Study of ARMC9 Gene Variants with Vogt-Koyanagi-Harada Disease in Japanese Patients.
    2. Our report of variant in ARMC9 Leading to Joubert syndrome phenotype (JS30), elucidates the genetic heterogeneity of Joubert syndrome, and expands the gene list for ciliopathies.
      Title: Whole exome sequencing reveals a mutation in ARMC9 as a cause of mental retardation, ptosis, and polydactyly.
    3. ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis.
      Title: Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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
    Joubert syndrome 30
    MedGen: C4539937 OMIM: 617622 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    EBI GWAS Catalog
    Genome-wide association study of sex hormones, gonadotropins and sex hormone-binding protein in Chinese men.
    EBI GWAS Catalog
    Genome-wide genetic and transcriptomic investigation of variation in antibody response to dietary antigens.
    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)

    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

    Clone Names

    • FLJ12584

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in ciliary tip IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary tip ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 

    General protein information

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    Preferred Names
    lisH domain-containing protein ARMC9
    Names
    armadillo repeat-containing protein 9
    armadillo/beta-catenin-like repeats
    melanoma/melanocyte specific protein KU-MEL-1
    melanoma/melanocyte-specific tumor antigen KU-MEL-1

    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.

    mRNA and Protein(s)

    1. NM_001271466.4 → NP_001258395.2  lisH domain-containing protein ARMC9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738, KF510794
      Consensus CDS
      CCDS74666.1
      UniProtKB/Swiss-Prot
      A0A087X1I8, Q53TI3, Q6P162, Q7L594, Q7Z3E5, Q86WG2, Q96JF9, Q9H9R8
      UniProtKB/TrEMBL
      A0A804HIH2, A0A804HIU9
      Conserved Domains (2) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif
      PHA03309
      Location:657 → 818
      PHA03309; transcriptional regulator ICP4; Provisional

    2. NM_001291656.2 → NP_001278585.2  lisH domain-containing protein ARMC9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS2484.1
      UniProtKB/TrEMBL
      A0A2Q3DP09, A0A804HIH2, A0A804HIU9
      Related
      ENSP00000508405.1, ENST00000684432.1
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    3. NM_001352754.2 → NP_001339683.2  lisH domain-containing protein ARMC9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738, KF510794
      Consensus CDS
      CCDS74666.1
      UniProtKB/Swiss-Prot
      A0A087X1I8, Q53TI3, Q6P162, Q7L594, Q7Z3E5, Q86WG2, Q96JF9, Q9H9R8
      UniProtKB/TrEMBL
      A0A804HIH2, A0A804HIU9
      Related
      ENSP00000484804.1, ENST00000611582.5
      Conserved Domains (2) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif
      PHA03309
      Location:657 → 818
      PHA03309; transcriptional regulator ICP4; Provisional

    4. NM_001352755.2 → NP_001339684.2  lisH domain-containing protein ARMC9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS2484.1
      UniProtKB/TrEMBL
      A0A2Q3DP09, A0A804HIH2, A0A804HIU9
      Related
      ENSP00000507543.1, ENST00000684718.1
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    5. NM_001352756.2 → NP_001339685.2  lisH domain-containing protein ARMC9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS2484.1
      UniProtKB/TrEMBL
      A0A2Q3DP09, A0A804HIH2, A0A804HIU9
      Related
      ENSP00000507743.1, ENST00000683575.1
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    6. NM_001352757.2 → NP_001339686.2  lisH domain-containing protein ARMC9 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS92970.1
      UniProtKB/TrEMBL
      A0A804HIH2, A0A804HIU9, A0A804HJI1
      Related
      ENSP00000507513.1, ENST00000683271.1
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    7. NM_001352758.2 → NP_001339687.2  lisH domain-containing protein ARMC9 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS92970.1
      UniProtKB/TrEMBL
      A0A804HIH2, A0A804HIU9, A0A804HJI1
      Related
      ENSP00000507152.1, ENST00000682002.1
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    8. NM_001352759.2 → NP_001339688.2  lisH domain-containing protein ARMC9 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS92969.1
      UniProtKB/TrEMBL
      A0A804HIH2, A0A804HIU9, H7BZY2
      Related
      ENSP00000392086.2, ENST00000436339.6
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    9. NM_025139.6 → NP_079415.4  lisH domain-containing protein ARMC9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Consensus CDS
      CCDS2484.1
      UniProtKB/TrEMBL
      A0A2Q3DP09, A0A804HIH2, A0A804HIU9
      Related
      ENSP00000258417.5, ENST00000349938.8
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    RNA

    1. NR_148040.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC009407, AC018738
      Related
      ENST00000684565.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      231198631..231376848
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      231683119..231861312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z3E5.3 GenPept UniProtKB/Swiss-Prot:Q7Z3E5

    Gene LinkOut

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

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