ARMC9

Summary

ARMC9 (armadillo repeat containing 9, HGNC:20730) is a protein-coding gene on chromosome 2q37.1, encoding LisH domain-containing protein ARMC9 (Q7Z3E5). Involved in ciliogenesis.

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.

Source: NCBI Gene 80210 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Joubert syndrome 30 (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 2
• Clinical variants (ClinVar): 764 total — 27 pathogenic, 24 likely-pathogenic
• Phenotypes (HPO): 62
• MANE Select transcript: NM_001352754

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20730
Approved symbol	ARMC9
Name	armadillo repeat containing 9
Location	2q37.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12584, KIAA1868, ARM, KU-MEL-1
Ensembl gene	ENSG00000135931
Ensembl biotype	protein_coding
OMIM	617612
Entrez	80210

Gene structure

Transcript identifiers

Ensembl transcripts: 55 — 27 protein_coding, 10 retained_intron, 10 nonsense_mediated_decay, 8 protein_coding_CDS_not_defined

ENST00000349938, ENST00000424740, ENST00000428662, ENST00000436339, ENST00000440107, ENST00000446447, ENST00000467698, ENST00000469789, ENST00000481520, ENST00000482392, ENST00000486787, ENST00000488821, ENST00000611582, ENST00000682002, ENST00000682027, ENST00000682030, ENST00000682100, ENST00000682233, ENST00000682264, ENST00000682334, ENST00000682367, ENST00000682751, ENST00000683040, ENST00000683063, ENST00000683107, ENST00000683112, ENST00000683165, ENST00000683271, ENST00000683275, ENST00000683321, ENST00000683520, ENST00000683553, ENST00000683575, ENST00000683629, ENST00000683702, ENST00000683814, ENST00000683966, ENST00000684011, ENST00000684051, ENST00000684075, ENST00000684224, ENST00000684368, ENST00000684432, ENST00000684565, ENST00000684718, ENST00000909243, ENST00000909244, ENST00000909245, ENST00000909246, ENST00000915562, ENST00000958131, ENST00000958132, ENST00000958133, ENST00000958134, ENST00000958135

RefSeq mRNA: 9 — MANE Select: NM_001352754 NM_001271466, NM_001291656, NM_001352754, NM_001352755, NM_001352756, NM_001352757, NM_001352758, NM_001352759, NM_025139

CCDS: CCDS2484, CCDS74666, CCDS92969, CCDS92970

Canonical transcript exons

ENST00000611582 — 25 exons

Exon	Start	End
ENSE00003465210	231216638	231216793
ENSE00003470249	231214831	231215001
ENSE00003473496	231272955	231273078
ENSE00003490778	231239943	231240041
ENSE00003531579	231270982	231271072
ENSE00003564689	231256586	231256620
ENSE00003573217	231226774	231226798
ENSE00003575323	231222728	231222820
ENSE00003576367	231282059	231282133
ENSE00003583978	231262306	231262398
ENSE00003616325	231206198	231206289
ENSE00003629643	231235224	231235381
ENSE00003631984	231258991	231259102
ENSE00003645052	231291353	231291443
ENSE00003668277	231296198	231296253
ENSE00003676922	231278382	231278458
ENSE00003682901	231208127	231208252
ENSE00003685604	231331793	231331897
ENSE00003712910	231360754	231360883
ENSE00003714689	231198631	231198698
ENSE00003716042	231369953	231370125
ENSE00003719652	231355798	231355934
ENSE00003731321	231344975	231345090
ENSE00003735728	231371513	231376848
ENSE00003789745	231276636	231276775

Expression profiles

Bgee: expression breadth ubiquitous, 244 present calls, max score 95.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.7642 / max 213.2320, expressed in 1645 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
25874	18.1535	1639
25875	1.5036	837
25883	0.0696	28
25881	0.0241	6
25880	0.0113	3
25882	0.0021	1

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	95.25	gold quality
secondary oocyte	CL:0000655	94.08	gold quality
oocyte	CL:0000023	93.98	gold quality
pigmented layer of retina	UBERON:0001782	93.04	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.33	gold quality
lower esophagus	UBERON:0013473	92.19	gold quality
buccal mucosa cell	CL:0002336	90.14	gold quality
left adrenal gland	UBERON:0001234	89.92	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	89.88	gold quality
left adrenal gland cortex	UBERON:0035825	89.72	gold quality
right adrenal gland	UBERON:0001233	89.21	gold quality
adrenal cortex	UBERON:0001235	89.13	gold quality
right adrenal gland cortex	UBERON:0035827	88.90	gold quality
adrenal gland	UBERON:0002369	88.75	gold quality
smooth muscle tissue	UBERON:0001135	88.45	gold quality
sural nerve	UBERON:0015488	87.92	gold quality
body of uterus	UBERON:0009853	87.80	gold quality
left ovary	UBERON:0002119	87.42	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.20	gold quality
tendon of biceps brachii	UBERON:0008188	86.62	gold quality
choroid plexus epithelium	UBERON:0003911	86.19	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.86	gold quality
ascending aorta	UBERON:0001496	85.85	gold quality
thoracic aorta	UBERON:0001515	85.59	gold quality
pituitary gland	UBERON:0000007	85.11	gold quality
ovary	UBERON:0000992	84.93	gold quality
myometrium	UBERON:0001296	84.91	gold quality
bronchial epithelial cell	CL:0002328	84.57	gold quality
right ovary	UBERON:0002118	84.50	gold quality
left testis	UBERON:0004533	84.50	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	19.30
E-ANND-3	yes	12.78
E-MTAB-6379	no	28.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

4 targeting ARMC9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-4720-3P	98.50	68.88	988

Literature-anchored findings (GeneRIF, showing 3)

• ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. (PMID:28625504)
• 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. (PMID:29159890)
• Our study suggests that ARMC9 variants do not play a critical role in the development of Vogt-Koyanagi disease. (PMID:30395750)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	armc9	ENSDARG00000087299
mus_musculus	Armc9	ENSMUSG00000062590
rattus_norvegicus	Armc9	ENSRNOG00000025418
caenorhabditis_elegans		WBGENE00019128

Protein

Protein identifiers

LisH domain-containing protein ARMC9 — Q7Z3E5 (reviewed: Q7Z3E5)

Alternative names: Armadillo repeat-containing protein 9, Melanoma/melanocyte-specific tumor antigen KU-MEL-1, NS21

All UniProt accessions (17): A0A2Q3DP09, A0A804HHZ1, A0A804HI20, A0A804HIH2, A0A804HIT2, A0A804HIU9, A0A804HJ52, A0A804HJ95, A0A804HJI1, A0A804HK42, A0A804HK85, Q7Z3E5, A0A804HL13, A0A804HLH5, C9JW07, H7BZA2, H7BZY2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in ciliogenesis. It is required for appropriate acetylation and polyglutamylation of ciliary microtubules, and regulation of cilium length. Acts as a positive regulator of hedgehog (Hh)signaling. May participate in the trafficking and/or retention of GLI2 and GLI3 proteins at the ciliary tip.

Subunit / interactions. Interacts with TOGARAM1, CCDC66, CEP104, CSPP1 and CEP290. Interacts with NDUFAF2.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium basal body. Cell projection. Cilium. Microtubule organizing center. Centrosome. Centriole.

Tissue specificity. Strongly expressed in most melanomas and melanocytes. Weakly expressed in the testis.

Disease relevance. Joubert syndrome 30 (JBTS30) [MIM:617622] A form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. JBTS30 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Induction. Up-regulated in response to serum starvation in fibroblasts.

Isoforms (2)

UniProt ID	Names	Canonical?
Q7Z3E5-1	1	yes
Q7Z3E5-2	2

RefSeq proteins (9): NP_001258395, NP_001278585, NP_001339683, NP_001339684, NP_001339685, NP_001339686, NP_001339687, NP_001339688, NP_079415 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006594	LisH	Conserved_site
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR040369	ARMC9	Family
IPR048957	ARMC9_LisH	Conserved_site
IPR048959	ARMC9_ARM_dom	Domain
IPR056327	ARMC9_CTLH-like_dom	Domain

Pfam: PF21050, PF21051, PF23138

UniProt features (22 total): sequence variant 11, region of interest 2, sequence conflict 2, compositionally biased region 2, chain 1, domain 1, coiled-coil region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z3E5-F1	71.71	0.33

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 582

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 220 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, ONKEN_UVEAL_MELANOMA_UP, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_REGULATION_OF_SMOOTHENED_SIGNALING_PATHWAY, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, APPIERTO_RESPONSE_TO_FENRETINIDE_DN, GOBP_SMOOTHENED_SIGNALING_PATHWAY, GOBP_CELL_PROJECTION_ORGANIZATION

GO Biological Process (3): positive regulation of smoothened signaling pathway (GO:0045880), cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (8): centriole (GO:0005814), ciliary basal body (GO:0036064), extracellular exosome (GO:0070062), ciliary tip (GO:0097542), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
microtubule organizing center	2
intracellular membraneless organelle	2
cilium	2
smoothened signaling pathway	1
regulation of smoothened signaling pathway	1
positive regulation of signal transduction	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
cellular component organization	1
binding	1
extracellular vesicle	1
intracellular anatomical structure	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

790 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMC9	TOGARAM1	Q9Y4F4	662
ARMC9	DPH5	Q9H2P9	569
ARMC9	KATNIP	O60303	540
ARMC9	ENOSF1	Q7L5Y1	497
ARMC9	RBM46	Q8TBY0	475
ARMC9	DRC7	Q8IY82	465
ARMC9	GID8	Q9NWU2	460
ARMC9	CEP104	O60308	439
ARMC9	C1orf216	Q8TAB5	434
ARMC9	INTS10	Q9NVR2	422
ARMC9	ARMC6	Q6NXE6	420
ARMC9	GLI2	P10070	407
ARMC9	CEP41	Q9BYV8	406
ARMC9	PAOX	Q6QHF9	402
ARMC9	CSPP1	Q1MSJ5	398
ARMC9	BRMS1	Q9HCU9	398

IntAct

34 interactions, top by confidence:

A	B	Type	Score
ARMC9	TOGARAM1	psi-mi:“MI:0915”(physical association)	0.700
TOGARAM1	ARMC9	psi-mi:“MI:0915”(physical association)	0.700
TOGARAM1	ARMC9	psi-mi:“MI:0403”(colocalization)	0.700
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
EPHA1	EXOC5	psi-mi:“MI:0914”(association)	0.530
ANKRD22	ESYT2	psi-mi:“MI:0914”(association)	0.530
SLC30A4	OPA1	psi-mi:“MI:0914”(association)	0.530
ARMC9	ARMC9	psi-mi:“MI:0915”(physical association)	0.510
NDUFAF2	ARMC9	psi-mi:“MI:0915”(physical association)	0.470
NDUFAF2	ARMC9	psi-mi:“MI:2364”(proximity)	0.470
ARMC9	NDUFAF2	psi-mi:“MI:2364”(proximity)	0.470
ARMC9	CCDC66	psi-mi:“MI:0915”(physical association)	0.400
CSPP1	ARMC9	psi-mi:“MI:0915”(physical association)	0.400
CEP104	ARMC9	psi-mi:“MI:0915”(physical association)	0.400
CCDC66	ARMC9	psi-mi:“MI:0915”(physical association)	0.400
CFTR	ARMC9	psi-mi:“MI:0915”(physical association)	0.370
GPR17	TMEM120B	psi-mi:“MI:0914”(association)	0.350
S100P	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
BTNL9	GPR89A	psi-mi:“MI:0914”(association)	0.350
TMEM167B	GLS	psi-mi:“MI:0914”(association)	0.350
RNF133	CD14	psi-mi:“MI:0914”(association)	0.350
CD40	IPO5	psi-mi:“MI:0914”(association)	0.350

BioGRID (26): ARMC9 (Two-hybrid), CMTM5 (Two-hybrid), ARMC9 (Affinity Capture-MS), KLHL8 (Two-hybrid), ARMC9 (Affinity Capture-MS), ARMC9 (Affinity Capture-MS), ARMC9 (Affinity Capture-MS), ARMC9 (Affinity Capture-MS), ARMC9 (Affinity Capture-MS), ARMC9 (Affinity Capture-MS), ARMC9 (Affinity Capture-MS), ARMC9 (PCA), ARMC9 (Proximity Label-MS), ARMC9 (Affinity Capture-MS), ARMC9 (Proximity Label-MS)

ESM2 similar proteins: A0A1L8F8I9, A0A2R8QPS5, A1A5P5, A7S2N8, B0BM28, B4FGS2, B8AXB6, B8B624, B8JKF4, B9FM64, F1QNV4, F4IQJ2, P49842, P97564, Q08CY4, Q08DB2, Q0P5W1, Q0VA04, Q14AI0, Q2KI89, Q32PH0, Q3SYG4, Q3U0M1, Q4R804, Q5R629, Q61586, Q66I84, Q68F70, Q6DHG8, Q6GL75, Q6GMB0, Q6GN08, Q6GPP1, Q6NU25, Q6PA97, Q7T006, Q7XAM0, Q7Z3E5, Q811G0, Q8CIM8

Diamond homologs: A0JMA8, A1A5P5, E7F187, Q2KI89, Q5R629, Q5U245, Q7Z3E5, Q9D2I5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

764 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	27
Likely pathogenic	24
Uncertain significance	344
Likely benign	275
Benign	47

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1034090	NM_001352754.2(ARMC9):c.100G>T (p.Glu34Ter)	Pathogenic
1069479	NC_000002.11:g.(?232137648)(232137811_?)del	Pathogenic
1076594	NM_001352754.2(ARMC9):c.1502del (p.Gly501fs)	Pathogenic
1397129	NM_001352754.2(ARMC9):c.574del (p.Thr192fs)	Pathogenic
1420862	NM_001352754.2(ARMC9):c.1418dup (p.Asp473fs)	Pathogenic
1431518	NM_001352754.2(ARMC9):c.162dup (p.Ser55fs)	Pathogenic
1453533	NM_001352754.2(ARMC9):c.895C>T (p.Arg299Ter)	Pathogenic
1454557	NM_001352754.2(ARMC9):c.1483_1484del (p.Met495fs)	Pathogenic
1458713	NC_000002.11:g.(?232209667)(232209822_?)del	Pathogenic
1909040	NM_001352754.2(ARMC9):c.1423dup (p.Thr475fs)	Pathogenic
1924081	NM_001352754.2(ARMC9):c.762_771del (p.Thr255fs)	Pathogenic
2018335	NM_001352754.2(ARMC9):c.1434C>G (p.Tyr478Ter)	Pathogenic
2024802	NM_001352754.2(ARMC9):c.1642del (p.Leu548fs)	Pathogenic
2091028	NM_001352754.2(ARMC9):c.1554dup (p.Gln519fs)	Pathogenic
2424077	NC_000002.11:g.(?232135675)(232135805_?)del	Pathogenic
2424079	NC_000002.11:g.(?232126999)(232141508_?)del	Pathogenic
2424080	NC_000002.11:g.(?232079524)(232091531_?)del	Pathogenic
3629018	NM_001352754.2(ARMC9):c.1515del (p.Val506fs)	Pathogenic
3648122	NC_000002.12:g.231256586del	Pathogenic
3693618	NM_001352754.2(ARMC9):c.1343dup (p.Gln449fs)	Pathogenic
3723653	NM_001352754.2(ARMC9):c.1246C>T (p.Gln416Ter)	Pathogenic
427933	NM_001352754.2(ARMC9):c.259C>T (p.Arg87Ter)	Pathogenic
427938	NM_001352754.2(ARMC9):c.1211-434_1335-1595delinsGTTTGTTTGTTTGTTTGCATTA	Pathogenic
4292717	NM_001352754.2(ARMC9):c.1878+1G>A	Pathogenic
4702604	NM_001352754.2(ARMC9):c.1102dup (p.Cys368fs)	Pathogenic
4722700	NM_001352754.2(ARMC9):c.1660G>T (p.Glu554Ter)	Pathogenic
953206	NM_001352754.2(ARMC9):c.1165C>T (p.Gln389Ter)	Pathogenic
1066488	NM_001352754.2(ARMC9):c.178-2A>G	Likely pathogenic
1323929	NM_001352754.2(ARMC9):c.178-2A>C	Likely pathogenic
1465530	NM_001352754.2(ARMC9):c.1119+1G>A	Likely pathogenic

SpliceAI

4568 predictions. Top by Δscore:

Variant	Effect	Δscore
2:231198696:CAGG:C	donor_loss	1.0000
2:231198697:AGGT:A	donor_loss	1.0000
2:231198699:GTAA:G	donor_loss	1.0000
2:231208125:A:AG	acceptor_gain	1.0000
2:231208126:G:GA	acceptor_gain	1.0000
2:231214829:A:AG	acceptor_gain	1.0000
2:231214829:AGAAG:A	acceptor_gain	1.0000
2:231214830:G:GG	acceptor_gain	1.0000
2:231214830:GAA:G	acceptor_gain	1.0000
2:231214830:GAAGG:G	acceptor_gain	1.0000
2:231214980:G:GT	donor_gain	1.0000
2:231214983:G:GG	donor_gain	1.0000
2:231216633:TCTA:T	acceptor_loss	1.0000
2:231216634:CTA:C	acceptor_loss	1.0000
2:231216636:A:AG	acceptor_gain	1.0000
2:231216636:A:AT	acceptor_loss	1.0000
2:231216636:AG:A	acceptor_gain	1.0000
2:231216637:G:A	acceptor_loss	1.0000
2:231216637:G:GA	acceptor_gain	1.0000
2:231216637:GG:G	acceptor_gain	1.0000
2:231216637:GGA:G	acceptor_gain	1.0000
2:231216637:GGAC:G	acceptor_gain	1.0000
2:231216789:TCCAG:T	donor_loss	1.0000
2:231216790:CCAG:C	donor_loss	1.0000
2:231216791:CAG:C	donor_loss	1.0000
2:231216792:AG:A	donor_loss	1.0000
2:231216793:GGT:G	donor_loss	1.0000
2:231216794:GTAA:G	donor_loss	1.0000
2:231216795:T:G	donor_loss	1.0000
2:231235210:AACT:A	acceptor_gain	1.0000

AlphaMissense

5362 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:231216741:T:C	L151P	0.999
2:231235344:T:C	L248P	0.999
2:231216738:C:A	A150D	0.998
2:231235323:T:C	L241P	0.998
2:231273071:A:C	S443R	0.998
2:231273073:T:A	S443R	0.998
2:231273073:T:G	S443R	0.998
2:231276758:T:C	L486P	0.998
2:231216750:T:A	V154D	0.997
2:231235337:G:C	A246P	0.997
2:231235356:T:C	L252P	0.997
2:231259038:T:C	L321P	0.997
2:231259095:T:C	L340P	0.997
2:231262307:G:C	R343P	0.997
2:231271043:T:C	L394P	0.997
2:231273060:T:C	L439P	0.997
2:231276775:G:T	G492W	0.997
2:231278436:T:C	L510P	0.997
2:231282084:T:C	L526P	0.997
2:231282122:G:C	A539P	0.997
2:231291369:T:C	L548P	0.997
2:231331889:T:G	Y624D	0.997
2:231216741:T:A	L151H	0.996
2:231216746:T:C	F153L	0.996
2:231216748:T:A	F153L	0.996
2:231216748:T:G	F153L	0.996
2:231216776:T:C	F163L	0.996
2:231216778:T:A	F163L	0.996
2:231216778:T:G	F163L	0.996
2:231259091:G:C	A339P	0.996

dbSNP variants (sampled 300 via entrez): RS1000010498 (2:231204948 C>T), RS1000046006 (2:231245659 T>C), RS1000047487 (2:231326607 T>C), RS1000050270 (2:231375087 C>T), RS1000059971 (2:231279067 G>A), RS1000097807 (2:231308750 T>C), RS1000158963 (2:231320616 T>C), RS1000168574 (2:231359376 C>T), RS1000206486 (2:231243510 A>G), RS1000230498 (2:231211245 G>A), RS1000247842 (2:231202185 A>C,G), RS1000256764 (2:231272763 G>A,C,T), RS1000293631 (2:231198678 G>T), RS1000294086 (2:231225377 A>G,T), RS1000297400 (2:231289974 A>G)

Disease associations

OMIM: gene MIM:617612 | disease phenotypes: MIM:617622, MIM:213300, MIM:220200, MIM:217990

GenCC curated gene-disease

Disease	Classification	Inheritance
Joubert syndrome 30	Definitive	Autosomal recessive
Joubert syndrome	Supportive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
Joubert syndrome 30	Definitive	AR

Mondo (5): Joubert syndrome 30 (MONDO:0033308), Joubert syndrome (MONDO:0018772), Dandy-Walker syndrome (MONDO:0009072), diabetes mellitus (MONDO:0005015), corpus callosum, agenesis of (MONDO:0009022)

Orphanet (3): Isolated Joubert syndrome (Orphanet:475), Isolated Dandy-Walker malformation (Orphanet:217), Isolated corpus callosum agenesis (Orphanet:200)

HPO phenotypes

62 total (30 of 62 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000054	Micropenis
HP:0000193	Bifid uvula
HP:0000202	Orofacial cleft
HP:0000218	High palate
HP:0000219	Thin upper lip vermilion
HP:0000238	Hydrocephalus
HP:0000276	Long face
HP:0000347	Micrognathia
HP:0000369	Low-set ears
HP:0000426	Prominent nasal bridge
HP:0000431	Wide nasal bridge
HP:0000463	Anteverted nares
HP:0000486	Strabismus
HP:0000496	Abnormality of eye movement
HP:0000508	Ptosis
HP:0000556	Retinal dystrophy
HP:0000589	Coloboma
HP:0000609	Optic nerve hypoplasia
HP:0000612	Iris coloboma
HP:0000639	Nystagmus
HP:0000657	Oculomotor apraxia
HP:0000750	Delayed speech and language development
HP:0000864	Abnormality of the hypothalamus-pituitary axis
HP:0001161	Hand polydactyly
HP:0001162	Postaxial hand polydactyly
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001252	Hypotonia

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002518_4	Food antigen IgG levels	1.000000e-06
GCST010917_4	Proportion of activated microglia (midfrontal cortex)	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005844	response to dietary antigen

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D061085	Agenesis of Corpus Callosum	C10.500.034; C16.131.666.034; C23.300.008
D003616	Dandy-Walker Syndrome	C10.228.140.252.300; C10.228.140.602.500; C10.500.205; C16.131.666.205
D003920	Diabetes Mellitus	C18.452.394.750; C19.246

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases expression	4
Tetrachlorodibenzodioxin	affects cotreatment, increases expression, affects expression	3
bisphenol A	decreases methylation, increases expression	2
sodium arsenite	affects cotreatment, decreases expression, increases abundance	2
Smoke	decreases expression, increases abundance, increases expression	2
Tretinoin	decreases expression, increases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
uranyl acetate	increases expression	1
pirinixic acid	decreases expression, increases activity, affects binding	1
lead acetate	affects cotreatment, decreases expression	1
trichostatin A	affects expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	affects methylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
incobotulinumtoxinA	increases expression	1
NSC 689534	affects binding, decreases expression	1
Dasatinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Arsenic	decreases expression, increases abundance, affects cotreatment	1
Copper	decreases expression, affects binding	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	increases expression	1
Endosulfan	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00044746	PHASE4	COMPLETED	Study Evaluating the Safety and Efficacy of Piperacillin/Tazobactam and Ampicillin/Sulbactam in Patients With Diabetic Foot Infections
NCT00069602	PHASE4	COMPLETED	Assessing Continuous Glucose Monitors in Healthy Children
NCT00079638	PHASE4	COMPLETED	Comparative Efficacy Evaluation of Lipids When Treated With Niaspan & Statin or Other Lipid-Modifying Therapies-COMPELL
NCT00095446	PHASE4	COMPLETED	NovoLog Observation Trial in Subjects With Type 1 and Type 2 Diabetes
NCT00101751	PHASE4	COMPLETED	INITIATE Plus (INITiation of Insulin to Reach A1c TargEt) Study
NCT00108615	PHASE4	COMPLETED	Effects of Insulin Sensitizers in Subjects With Impaired Glucose Tolerance
NCT00117780	PHASE4	COMPLETED	Comparison of Insulin Detemir Given Once or Twice Daily in Type 1 Diabetes
NCT00120341	PHASE4	COMPLETED	Anodyne Therapy in Diabetic Sensory Neuropathy
NCT00121355	PHASE4	COMPLETED	Novofine Autocover Safety Needle Versus BD Safety Glide
NCT00135226	PHASE4	ACTIVE_NOT_RECRUITING	ASCEND: A Study of Cardiovascular Events iN Diabetes
NCT00144937	PHASE4	UNKNOWN	Multifactorial Intervention on Cardiovascular Risk Factors in Subjects With Peripheral Arterial Disease
NCT00147251	PHASE4	COMPLETED	Stop Atherosclerosis in Native Diabetics Study
NCT00157638	PHASE4	COMPLETED	Integrating Family Medicine and Pharmacy to Advance Primary Care Therapeutics
NCT00162344	PHASE4	COMPLETED	A Study of Stress Heart Imaging in Patients With Diabetes at Risk for Coronary Disease.
NCT00177138	PHASE4	TERMINATED	Use of Campath for Induction and Maintenance Therapy in Pancreas After Kidney Transplantation
NCT00182494	PHASE4	UNKNOWN	Diabetes Prevention Program in Schizophrenia [DPPS]
NCT00184561	PHASE4	COMPLETED	Effectiveness and Safety of Biphasic Insulin Aspart 70/30 in Subjects With Type 2 Diabetes
NCT00184626	PHASE4	COMPLETED	Comparison of Insulin Glargine Versus Biphasic Insulin Aspart 30/70 or Biphasic Insulin Aspart 30/70 in Combination With Metformin in Subjects With Type 2 Diabetes.
NCT00202618	PHASE4	UNKNOWN	Rationale and Design for Shiga Microalbuminuria Reduction Trial
NCT00209170	PHASE4	COMPLETED	Depression-Diabetes Mechanisms: Urban African Americans
NCT00209417	PHASE4	TERMINATED	Renal Effects of Two Iodinated Contrast Media in Patients at Risk Undergoing Computed Tomography
NCT00212004	PHASE4	TERMINATED	Pioglitazone Protects Diabetes Mellitus (DM) Patients Against Re-Infarction (PPAR Study)
NCT00219440	PHASE4	COMPLETED	A Portion-controlled Diet Will Prevent Weight Gain in Diabetics Treated With ACTOS
NCT00225849	PHASE4	UNKNOWN	Japanese Primary Prevention Project With Aspirin
NCT00231894	PHASE4	COMPLETED	Pioglitazone as a Treatment for Lipid and Glucose Abnormalities In Patients With Schizophrenia
NCT00234871	PHASE4	COMPLETED	Tarka® vs. Lotrel® in Hypertensive, Diabetic Subjects With Renal Disease (TANDEM)
NCT00235014	PHASE4	COMPLETED	A Study for Prevention of Kidney Disease in Diabetic Patients (BENEDICT)
NCT00236379	PHASE4	COMPLETED	A Study of the Effects of Risperidone and Olanzapine on Blood Glucose (Sugar) in Patients With Schizophrenia or Schizoaffective Disorder
NCT00241904	PHASE4	COMPLETED	Reducing Total Cardiovascular Risk in an Urban Community
NCT00263393	PHASE4	COMPLETED	Rural Andhra Pradesh Cardiovascular Prevention Study (RAPCAPS)
NCT00264901	PHASE4	COMPLETED	Comparison of Self Adjustment Versus Standard of Care Treatment in Subjects With Type 2 Diabetes
NCT00274274	PHASE4	COMPLETED	Efficacy and Safety of a Fixed or a Flexible Supplementary Insulin Therapy in Type 2 Diabetes
NCT00282451	PHASE4	COMPLETED	Effect of Biphasic Insulin Compared to Biphasic Insulin Combined With Insulin Aspart, With or Without Metformin in Type 2 Diabetes
NCT00282659	PHASE4	COMPLETED	The Use of Magnesium to Improve Blood Pressure, Cholesterol, and Glucose Control
NCT00287820	PHASE4	COMPLETED	Comparative Effects of Chronic Treatment With Olanzapine and Risperidone on Glucose and Lipid Metabolism
NCT00295555	PHASE4	COMPLETED	Doxazosin Effects on ABPM in Hypertensive Patients With Diabetic Nephropathy
NCT00299169	PHASE4	TERMINATED	Randomized Trial Comparing N of 1 Trials to Standard Practice to Improve Adherence to Statins in Patients With Diabetes
NCT00301392	PHASE4	COMPLETED	Japan Prevention Trial of Diabetes by Pitavastatin in Patients With Impaired Glucose Tolerance (J-PREDICT)
NCT00306696	PHASE4	COMPLETED	Examining the Effect of Different Diuretics on Fluid Retention in Diabetics Treated With Rosiglitazone.
NCT00309465	PHASE4	COMPLETED	Perioperative Insulin Glargine Dosing Study