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

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
ARMC9-related Joubert syndrome	Pathogenic; Likely pathogenic	rs372770167, rs759799287, rs753432312, rs780265931, rs1114167448, rs1114167449	RCV000490944 RCV000491717 RCV000490882 RCV000491687 RCV000491387 RCV000490913	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Dandy-Walker syndrome	Likely pathogenic; Pathogenic	rs759799287, rs780265931	RCV001257947 RCV001257948	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome	Pathogenic; Likely pathogenic	rs372770167, rs759799287, rs753432312, rs780265931, rs1114167448, rs1114167449	RCV001034534 RCV001034537 RCV001034533 RCV001034540 RCV001034539 RCV001034541	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Malignant tumor of urinary bladder	Pathogenic	rs1189780573	RCV005909068	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ARMC9-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corpus callosum, agenesis of	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes mellitus	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
DIVERTICULAR DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE MYELOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	BEFREE	15370542, 16123405, 18235016, 28387762, 30820012		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	11691810		★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet Syndrome	BEFREE	16481377		★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Endometrioid	Endometrioid carcinoma	Pubtator	16394288	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37480570	Associate	★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	29391492		★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	28625504, 29159890		★☆☆☆☆ Found in Text Mining only
Congenital cerebral hernia	Congenital Cerebral Hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Currarino triad	Currarino Triad	BEFREE	28065719		★☆☆☆☆ Found in Text Mining only
Depressive disorder	Mental Depression	BEFREE	28732243		★☆☆☆☆ Found in Text Mining only
Dermatitis	Dermatitis	BEFREE	31146741		★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Diabetic Retinopathy	BEFREE	28387762		★☆☆☆☆ Found in Text Mining only
Ependymoma	Ependymoma	BEFREE	27637901		★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	28625504, 29159890		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	GENOMICS_ENGLAND_DG	28625504		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	ORPHANET_DG	28625504		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fecal Incontinence	Bowel incontinence	BEFREE	27696628		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glycogen storage disease type II	Glycogen Storage Disease	BEFREE	28387762		★☆☆☆☆ Found in Text Mining only
Head and Neck Carcinoma	Head And Neck Carcinoma	BEFREE	31146741		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	28625504		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	29159890		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Joubert syndrome	Joubert syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome 1	Joubert Syndrome	ORPHANET_DG	28625504		★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 30	Joubert syndrome	GENOMICS_ENGLAND_DG	28625504		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 30	Joubert syndrome	UNIPROT_DG	28625504		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 30	Joubert syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Liver Cirrhosis Biliary	Liver cirrhosis	Pubtator	11559656	Associate	★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	12937339	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Head and Neck Neoplasm	Head and neck cancer	BEFREE	31146741		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	11691810		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Melanoma	Pubtator	16481377	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental Depression	Mental Depression	BEFREE	28732243		★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	29159890		★☆☆☆☆ Found in Text Mining only
Mucopolysaccharidosis Type IIIA	Mucopolysaccharidosis	BEFREE	20370351		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	11691810		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculovestibuloauditory syndrome	Oculovestibuloauditory Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oral cleft	Oral cleft	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	BEFREE	31543421		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	BEFREE	29159890		★☆☆☆☆ Found in Text Mining only
Polydactyly of toes	Polydactyly Of Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Situs inversus totalis	Situs Inversus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Uveomeningoencephalitic Syndrome	Uveomeningoencephalitic Syndrome	BEFREE	16481377		★☆☆☆☆ Found in Text Mining only
Uveomeningoencephalitic Syndrome	Uveomeningoencephalitic syndrome	Pubtator	16481377	Associate	★☆☆☆☆ Found in Text Mining only