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

    Gene ID: 80210, updated on 7-Jan-2024

    Summary

    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, Apr 2022]
    Expression
    Broad expression in endometrium (RPKM 2.3), ovary (RPKM 1.9) and 22 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See ARMC9 in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (231198631..231376848)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231683119..231861312)
    105.20220307 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Joubert syndrome 30
    MedGen: C4539937 OMIM: 617622 GeneReviews: Not available
    Compare labs

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001271466.4NP_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:738
      LisH; Lissencephaly type-1-like homology motif
      PHA03309
      Location:657818
      PHA03309; transcriptional regulator ICP4; Provisional
    2. NM_001291656.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
    3. NM_001352754.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
      PHA03309
      Location:657818
      PHA03309; transcriptional regulator ICP4; Provisional
    4. NM_001352755.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
    5. NM_001352756.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
    6. NM_001352757.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
    7. NM_001352758.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
    8. NM_001352759.2NP_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:738
      LisH; Lissencephaly type-1-like homology motif
    9. NM_025139.6NP_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:738
      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_2023_10

    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)