ARMC9 (armadillo repeat containing 9)

Gene

• Entrez ID: 80210
• Gene name: Armadillo repeat containing 9
• Gene symbol: ARMC9
• Synonyms (NCBI Gene): ARM, JBTS30, KU-MEL-1, NS21
• Chromosome: 2
• Chromosome location: 2q37.1

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs372770167	C>A,T	Pathogenic	Genic upstream transcript variant, stop gained, non coding transcript variant, synonymous variant, coding sequence variant
rs750247691	G>A	Pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs753432312	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs759799287	C>A,T	Pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs766572502	G>A	Likely-pathogenic	Non coding transcript variant, intron variant, genic upstream transcript variant, coding sequence variant, synonymous variant
rs780265931	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1114167447	G>T	Pathogenic	Genic upstream transcript variant, intron variant
rs1114167448	G>C	Pathogenic	Splice donor variant
rs1114167449	C>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT799309	hsa-miR-1323	CLIP-seq
MIRT799310	hsa-miR-548o	CLIP-seq
MIRT799311	hsa-miR-600	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25416956, 32296183, 32453716, 38949024
GO:0005737	Component	Cytoplasm	IEA
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IDA	28625504
GO:0005814	Component	Centriole	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0036064	Component	Ciliary basal body	IBA
GO:0036064	Component	Ciliary basal body	IDA	28625504
GO:0036064	Component	Ciliary basal body	IEA
GO:0042995	Component	Cell projection	IEA
GO:0045880	Process	Positive regulation of smoothened signaling pathway	IEA
GO:0045880	Process	Positive regulation of smoothened signaling pathway	ISS
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	ISS
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0097542	Component	Ciliary tip	IBA
GO:0097542	Component	Ciliary tip	IEA
GO:0097542	Component	Ciliary tip	ISS

Other IDs

• MIM: 617612
• HGNC: 20730
• e!Ensembl: ENSG00000135931

Protein

• UniProt ID: Q7Z3E5
• Protein name: LisH domain-containing protein ARMC9 (Armadillo repeat-containing protein 9) (Melanoma/melanocyte-specific tumor antigen KU-MEL-1) (NS21)
• Protein function: Involved in ciliogenesis (PubMed:32453716). It is required for appropriate acetylation and polyglutamylation of ciliary microtubules, and regulation of cilium length (PubMed:32453716). Acts as a positive regulator of hedgehog (Hh)signaling (By s
• Tissue specificity: TISSUE SPECIFICITY: Strongly expressed in most melanomas and melanocytes. Weakly expressed in the testis. {ECO:0000269|PubMed:11691810}.
• Sequence:

  MGDILAHESELLGLVKEYLDFAEFEDTLKTFSKECKIKGKPLCKTVGGSFRDSKSLTIQK
  DLVAAFDNGDQKVFFDLWEEHISSSIRDGDSFAQKLEFYLHIHFAIYLLKYSVGRPDKEE
  LDEKISYFKTYLETKGAALSQTTEFLPFYALPFVPNPMVHPSFKELFQDSWTPELKLKLI
  KFLALISKASNTPKLLTIYKENGQSNKEILQQLHQQLVEAERRSVTYLKRYNKIQADYHN
  LIGVTAELVDSLEATVSGKMITPEYLQSVCVRLFSNQMRQSLAHSVDFTRPGTASTMLRA
  SLAPVKLKDVPLLPSLDYEKLKKDLILGSDRLKAFLLQALRWRLTTSHPGEQRETVLQAY
  ISNDLLDCYSHNQRSVLQLLHSTSDVVRQYMARLINAFASLAEGRLYLAQNTKVLQMLEG
  RLKEEDKDIITRENVLGALQKFSLRRPLQTAMIQDGLIFWLVDVLKDPDCLSDYTLEYSV
  ALLMNLCLRSTGKNMCAKVAGLVLKVLSDLLGHENHEIQPYVNGALYSILSVPSIREEAR
  AMGMEDILRCFIKEGNAEMIRQIEFIIKQLNSEELPDGVLESDDDEDEDDEEDHDIMEAD
  LDKDELIQPQLGELSGEKLLTTEYLGIMTNTGKTRRKGLANVQWSGDEPLQRPVTPGGHR
  NGYPVVEDQHTPPQTAQHARNGHPQALPAAHEAVYREGKPSTPESCVSSSSAIIAKPGEW
  LPRGRQEEPRPAPTGTPRQPREAPQDPGNGVTTRECASAFTCKPRAPCTPEMLDWNPPKA
  KASVLAPLFSSCGPQQASRPGSTASSTRGLPSSQSHRK

• Sequence length: 818

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
ARMC9-related Joubert syndrome	Pathogenic; Likely pathogenic	rs372770167, rs759799287, rs753432312, rs780265931, rs1114167448, rs1114167449	RCV000490944 RCV000491717 RCV000490882 RCV000491687 RCV000491387 RCV000490913
Dandy-Walker syndrome	Likely pathogenic; Pathogenic	rs759799287, rs780265931	RCV001257947 RCV001257948
Joubert syndrome	Pathogenic; Likely pathogenic	rs372770167, rs759799287, rs753432312, rs780265931, rs1114167448, rs1114167449	RCV001034534 RCV001034537 RCV001034533 RCV001034540 RCV001034539 RCV001034541
Joubert syndrome 30	Pathogenic; Likely pathogenic	rs1330612935, rs1248147660, rs754385274, rs1331571804, rs372770167, rs759799287, rs753432312, rs780265931, rs1114167448, rs1114167449, rs766572502	RCV001336697 RCV001785962 RCV005225550 RCV006437153 RCV000515482 RCV000515505 RCV000515503 RCV000515496 RCV000515484 RCV000515485 RCV000625743
Malignant tumor of urinary bladder	Pathogenic	rs1189780573	RCV005909068

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Benign	rs115179589	RCV005914108
Adrenocortical carcinoma, hereditary	Benign	rs35643982	RCV005909685
ARMC9-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	rs202164814, rs779365675, rs138398575, rs527487315, rs146650763, rs148296188, rs148607124, rs781559742, rs1219700669, rs2470033379, rs2045327588, rs144026971, rs59475942, rs116712981, rs150092118, rs775687932, rs146934178, rs61753914, rs146743949, rs114592321, rs536000748	RCV003963232 RCV003953714 RCV003900472 RCV003956075 RCV004757458 RCV003921143 RCV003940924 RCV003892885 RCV004757501 RCV003894410 RCV003902073 RCV003970774 RCV003926172 RCV003926156 RCV003928532 RCV003910494 RCV003910763 RCV003922989 RCV003903240 RCV003972946 RCV003953457
Cervical cancer	Benign; Likely benign	rs115179589, rs144026971	RCV005914110 RCV005908222
Cholangiocarcinoma	Benign	rs35643982	RCV005909691
Clear cell carcinoma of kidney	Benign	rs115179589	RCV005914111
Colorectal cancer	Benign	rs35643982	RCV005909687
Corpus callosum, agenesis of	Conflicting classifications of pathogenicity	rs201590882	RCV001007925
Diabetes mellitus	Conflicting classifications of pathogenicity	rs201590882	RCV001007925
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	rs2045319341	RCV004557826
Familial cancer of breast	Likely benign	rs373903250	RCV005912702
Familial pancreatic carcinoma	Benign	rs115179589	RCV005914113
Familial prostate cancer	Uncertain significance	rs781051576	RCV005922877
Gastric cancer	Benign; Likely benign	rs115179589, rs754616310	RCV005914115 RCV005926329
Hepatocellular carcinoma	Uncertain significance; Likely benign	rs781051576, rs144026971	RCV005922876 RCV005908221
Lung cancer	Benign	rs115179589	RCV005914118
Malignant tumor of esophagus	Benign	rs115179589	RCV005914109
Melanoma	Likely benign	rs144026971	RCV005908223
Nonpapillary renal cell carcinoma	Benign	rs35643982	RCV005909684
Ovarian serous cystadenocarcinoma	Benign	rs115179589	RCV005914116
Sarcoma	Benign	rs35643982, rs115179589	RCV005909688 RCV005914114
See cases	Benign	rs386656198	RCV002252686
Thymoma	Benign; Uncertain significance	rs35643982, rs190810391	RCV005909690 RCV005912436
Thyroid cancer, nonmedullary, 1	Uncertain significance	rs750286873	RCV005928387
Uterine carcinosarcoma	Benign	rs35643982, rs115179589	RCV005909689 RCV005914117
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	rs35643982, rs190810391	RCV005909692 RCV005912437
Uveal melanoma	Benign	rs35643982, rs115179589	RCV005909686 RCV005914112

Associations from Text Mining
Disease Name	Relationship Type	References
Carcinoma Hepatocellular	Associate	37480570
Melanoma	Associate	16481377
Uveomeningoencephalitic Syndrome	Associate	16481377