ARMC9

armadillo repeat containing 9, the group of MicroRNA protein coding host genes|Armadillo repeat containing

Basic information

Region (hg38): 2:231198546-231376848

Links

ENSG00000135931

∙ NCBI:80210 ∙ OMIM:617612 ∙ HGNC:20730 ∙ Uniprot:Q7Z3E5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Joubert syndrome 30 (Strong), mode of inheritance: AR
Joubert syndrome (Supportive), mode of inheritance: AR
Joubert syndrome 30 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 30	AR	Endocrine	The condition has been described as involving panhypopituitarism, and awareness may allow early diagnosis and medical management (eg, with hormone replacement therapy)	Endocrine; Musculoskeletal; Neurologic; Ophthalmologic	28625504

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARMC9 gene.

not provided (14 variants)
Joubert syndrome 30 (2 variants)
Familial aplasia of the vermis (1 variants)
ARMC9-related Joubert syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMC9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			8 clinvar	122 clinvar	12 clinvar	142
missense		2 clinvar	279 clinvar	8 clinvar	13 clinvar	302
nonsense	5 clinvar		3 clinvar			8
start loss						0
frameshift	10 clinvar		3 clinvar		1 clinvar	14
inframe indel			7 clinvar			7
splice donor/acceptor (+/-2bp)		17 clinvar	3 clinvar			20
splice region		1	19	21	5	46
non coding			8 clinvar	78 clinvar	18 clinvar	104
Total	15	19	311	208	44

Highest pathogenic variant AF is 0.0000329

Variants in ARMC9

This is a list of pathogenic ClinVar variants found in the ARMC9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
2-231203676-AAGGCTGGGCGTGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACGTGGTAAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTAGGCATGGTGGCGGGTGCCTGTAATCCCAGCTACTCGGGAGGCTGAAGCAGGAGAATTGCTGGAACCCCGGAGGTGGAGGTTGCAGTGAGCCAAGATTGTGCCATTCTACTCCAGCCCAAGCAACAACAGCGAGACTCTGTCTCAAAAACAAACAAACAAAAAAAAACCTCACCAAAAACCAAACAAATGAAAAAACCAGAAAACAAAAGACTTGGGGCATAGTGGCACACTCTGTAGGCCCAGCTACTCAGGAGGCTGAGGTGGGAGGACTGCTTGAGTCCAGGAGTTTGAGGCTGCAGTGAGCTATGATCATGTCACTGCACTCTAGCCTGGGCAACAGAGGGAAACTCTGTCTCAGGAAAAAAAAAAAAAAAAAAAAAGGACATCAGTGGTGTCAGTCCCCTCCTCCATACTCTCTCTGAGCCTCCTGTTACTGTCAGCCTAATGTCCAAGCCACTTACCAGCTCTGTAAGGCCCACCTGACCTGGCCCCGGCCCCCCATTGCCTGCTGCTGTCTGCCTCACCCCTAGCTACATCCCAATACCCCAAGACTGCAGAGCTCTTCAGCCTGAGGCCTGTGCACTAACAAAGCCATCTTCCCCAGATCCAGGTGCTCAATCTTTGCTGAAATGTCACATTCCCAGTGAGGCCATCAACCACTCTATCTAAAATAACCCCATACCCGTCTCCTTCAGGTTCTGTCCCTTTCCTTGCGCTGTTTTCTTCATGTCTGGAATCAATTTCCACTCCGTCCATGTTTTTGAGCCTGTACTGTGTGCCAGGCACTGGTCTAGGCACAGGGGAACACCTGTCAGGTGCTGTTGAGAAAAATCAAGCAGTACAAAGGGCTGAGAAGTGATGGGCCGACCTCTTAGAAAGGGTGGTCAGGGCAAGACTCTCTGAGGAGGTGACAGTTAGGCAGAGACCTGAATGAGACGTATCTGAAGGAAGGGCAGTGAGCCAGAGTTCACGAGGGCAGGCGTGTGCTTTGGGTGTTCAGTGGGTGTCCACAGGAACCACACAGTGGCCAGTGTGGCTCAGGTTTACAGAACAAATGGGAGTGTGTCAGAGGCCAAGTTGTCTAGGGCTTTGGGAGTTGAGCCTAAGGAGCCTGGCCTTCATCTGGAGGGCGCTGGAACCACAGGAGGGTCCCAAGCAGGAGGGGAATGCTCACTTGTTAAAAGTGTAGAAATTGGATTGAAGTGGAGAGAAAGGAGGTGGGGAGGCAGTGGCAGAAAAATGTAAGGTTACAGACTCAGAAGAGATCTGACTGAGTGTGGTGGCTCACGCCTATAATCCCAGCATTTTGGGAGGCCAAGGCGGGAGGATTGCATTACCCAGGAGTTTGGCAGCTTAGTAAGACCCTGTCTCCCTGTCTCTACTTAAAAAAAAAAAAAAAAAAATTACCTGGGTATGGTGGCATGCACCTATAGTTCTAGCCACTGGGGAGGCTGAGGAGGGAGGATCCCTTGAACCCAGGAGTTTTAGCTTGCAGTGAGCTATGATTGCACCATTGCACTCCATCCTGGGCAACGGAGTGAGATCCCATCTCAAAAAAAAAATTCGATGAGTTCTGACACATTCTGAATTTTATAGATGAAGAAAGGCTCTGCACTTCAGTGAGTTGTCTCAGATCAGGTGCCAGTGAATGGCATGGTTAACATTAGAGCCCAGACCTTTTCATTCCTCTGGGGTTACGGGCAACTGCTTTGGGCTGAGCCTGGGGTGTGGGCCATGGGGAATGACTGCTTTGGGTACACCTTGAGGGAGGGCTAGTAGAAAGAGTAGGAAGAGTTTCTTTTGACTTTAGCCATTGTATTTCCTAGTGCCGCTGAACAAATGACCATAAACTGAGTGGTGTCAAGCAACAAAGATTTAATATCTTCTAGTTCTGGAGGTCAGAAGTCTGAAATGGCTTTCACTGAGCTGAAGTCAAGGTGTCTGCAGTGCTGGATCATTTCTGGATGCAGTGGGAGGATCTATTCCTTGCCTTATGCAGTTTTTAGAGGCTCCTTACCCTCCTTGTCTTATGCCACTTTATCCCCTTTAAAGCCTGCAGTGGCTGTTGAGTCTTTCTCACATCTCATCATGCTGGCACTGACCCTCTTGCCTCCGTCTGCCCCCCTCCCTCTGCTGTGACTGCCTTGGGCCCACCTGGGTAATCCAGGATCATCCCCCAATTTAAAGGTCAGCTGATGAGCAACCTTAATTCCATCTGCACCTTAATTCCCCCTTGCCGTGTAACCTCACGTATTCACAGGTTCTGGGGATTGGCGCATGGATGTCTTTGGGGGCCATTATTCTGCTCACCACAACCACCTTTTTGTAGTTTCATAGGTGGTTGAAATGAAAGCTGTTGTCTTGTATTTTTGCCTTCTAGAGATTTTTGCTGTGAGAATTAATTACCAGTAACAGTTCAATATGGGGGACATTCTGGCTCATGAATCTGAATTACTTGGACTAGTGAAAGAGGTAGGTATATTATACAAAGCAGAGGTCACAGAGAAACAGATCTTGAAAACTTGTGTTTTAAAATGCAACAAACTATTTAGTGCCTTGTAATGTTTCTTCTATTGTTATGTTGGAGCTATTTTTCTATTATATAATATTCCATGTATTTACATTTTGGTTTTATAACTAAACAAATCTTAAAGCCACTTAAAAAGTCCCTTGAAAGAAAATTATAAAAGCAATACACGTCCACGGTAAAAGATTCAAGCACTACAGAAGTATAAAAAGGAAATTTCCCTCCCAGACTTTTTTCTATGTATAGTAAAAATATATTCACATGCCTGTAGTTTGTTTTACAGAATGGGATGATACATTGTTCTGTAGCTTGCTTTTTATCTGCCAACAATAATATAGCATGAACATCTGCCTATGATCGGCCCTAGACATTTGAATGCCATAGAGTATTTCATTGAGTGGCTGCATCATAATTTTTTTAACTCATTGTCTGGTAATGGCCTAGGTTTCCTACGCTAAAAGCTTTGACAAGTAGGGCCCAGGCCTTAAACTTTCTGGTGCTAAAGAAATGGTTCGCGCTTGCTGCTGCTTAACTGTGTGAGTAACCACCTGCAGGTTGCGAGAGCCACGGGCCTGGAGCAGGGATGAGGCACCCACCGTGCAACTGCAGATTTGGAATTTGGTGGTGTGATGGCGAATATATTCTTTTTTAAAAAATTTACATTTAAAAATCTTTTTAGAGACAAGGTCTTGTTCTGCCGCCTAGGCTGGAGTGCAGTGGCATCATCATGGTTCACTGTAGCCTTGAACTCCTGGGCTCAAGCAATCTGCCTGCCTCAGCCTCCTGGGTAGCTGAGACTACAGACGTGCACCACCATGCTCAGCTAGGTTTTATTCTAATTTTTGTAGAGATAGGATCTCACTCTGTTGTCCAAGCTGGTCTTGAACTCTTGGCTTCAAGCAATCCTCCTGCCTCAGCCTCCCAAAGTTGTGGGATTGCAGGCATGAGCCACTGCACCCTACCTATATAACACATTTTCTTTTAAAAATTTATTTATTTGAGATGGGGTCTCGCTTTGTTGCCCAGGCTGGTCTCAAAGTCCTAGGCTCAAGCGATCCTCCTACCTCAGCCTCCCAAAGTGTTGGGATTACAGGCATGAGCCATGCCACCTGGCCTATACCATTTTTTCTTTTTTTTTTCTTTTTTTTTGAGATGGAGTCTCACTCTGTCGCCCAGGCAGGAGTACAGTGGTGCTTTCTCTGCTCACTGCAACCTCCACCTCCTGGGCTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACGCGCCACTGCGCCTGGCTAATTTTTGTATTTTCAGTAGAGACGGGGTTTCACCTTGCTGGCCAGGCTGGTCTCGAATTCCTGACCTCGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCTTGAGTCACGGCTCCTGGCCGGTAGTTCTATTTTTATTTTTTTGAGGAACCTCCATACAGTTTTCTATAATGGCCGTACCAATTTACAGTCTCACCAAGAGTGCACAAGTGTTTCCTTTTCTCCACATCCTTGCCAAGACTTTTTATCTTTCGTCTTTTTTGTAATAGCCATTCTGACAGGTGTGAGGTAATTAGGTCTCTGTGGTTTTGATTTGCATTTCTCTGATTGTTAGTGATGTTAAGCACCTTTTCATGTATCTGTTGGTCTTTTTAATGTCTTCTTTGGATAAATATCTATTCAGATCCTTTGGCTGTTTTTTAATTGGATTATTTGTTTGTTTTGCTGTTGAATTGAATTATTTATTTTTTATAGTATTTAGATTTTGCTGAATTTGAAGACACCTTGAAAACATTTTCAAAAGAATGCAAAATAAAAGGAAAACCATTGTGTAAAACAGTAGGCGGATCTTTCAGAGACTCCAAATCATTGACAATTCAGGTAACATTTTGCTTATTTTTCATCCCTGTAGATAATTCAGGATGCTCCCAACTTGTGGAAAATGCTGCTGTTGGATAGTGCTAGAATAGTTTTTGAGCACTTGCTCAGAGTTACTTTAGATGGCACAAGTGTTTATAGATGAACTAATAATGTCATTTTAAATCTCTGTACCCTCCCCAGGAAATGTGTGGCCATATAAGATCTTTCACAAACATTTCTTGGGAAGAAGGAAAAGAAGAAACCATGCAGTGTTTAGGAACTGAGACAATTGTAGCCTTCCTCCTGAGGAGTTTCAGGTTATTAATTCTAGGCACTGGGGATCCAGCAGTGAACAAACAAAATCCAGCCCCTTGCCAGCACAGCATTTGCATTCTAGCTTGGGGAGGTTGGAGGGAACAGGGAGCAAGAGTGAGACTGACAAGGCGGGTCTGTGAAAGGAAGTCTGAATAGCTCTGTGAATACCAGTGGGCTGCAGGGGCACAGAGGTTATACAGACCTCAACTCTCAGGGTTAGAAGGGACCTTAAAAATCCTTGACTAGGCATGGTGGCTGAATCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGAGGACCGCATAAACCCAGGAGTTCAAGACCAGCCTGTGCAACACAGTAGGACCTCGTTTCTTTTTCTTTTTTTTTGAGATGGAGTCTCTCGCTCTGTCGCCCAGGCTGGAGTGCGGTGGTACGATCTCGGCTCATCACCACCTCTGCCTCCAGGATTCAAGCGATTCTCCTGCCTCACCCTCCCTAGTAGCTAGGATTACAGGCACGTGCTACTGCGTCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACTACATTGGCCAGGCTAGTCTTGAACTCCTGACCTCAAGTGATCCGCCCGCCTTGGCCTCCCAAAAGTGCTGAGGTTACAGATGTGAGCCACCATGCCCAGCCAGAACCTCGTTTCTATAAAAAATAAAAAATTGGCCGAGCATGGTGGCATGCACCTGTAGTCCCAGCTACTTAGGTGGCTGAGGTAGGAGGATCACTTGAGCCTGGGAAATCAAGGCTGCATTGAGCCATGATCATACTGCTGCACTCCAGCTGTAGTGACAGAGTGAGACCCTGTCTCCAAAAAAATTAAAAAGTCATTATTTTAACCATTATTTGATGTCTAAATCTCATTTGTAATATGCCAGGTAAGTAATCAGTTCACCTAGAATATTTCCATTGACTAGAGACTGTACCATTTCCTGAGACAGCATGTTTCACATTTGGATGATTTTATTATTTATTTATGTATTTGAGACGGAGTTGCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCAGGATCTTGGCTTACTGCAACCCCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCACACACCATCATGCCCAGCTGGTTTTAGTATTTTTATTGGAGATAGGGTTTCACCAGGTTGGCCAGGCTGGTCTCAAACTCCTGACCTTTGGTGATCCACCCGCCTCAGCCTTCCAAAGTGCTGGGATTACAGATGTGGCCACCACACCTGGTCTATTTTATTTTTATAATTAAAAAAAATTATGTGGAGACAGGGTCTTGCTGTGTTTCCCAGGCTGGTCTCAAACTCCCAATCTCAAGTGATCTTCCTGCCTCAACCTCCCAAAGCACTGGGATTATAGGCATGAGCCACTGCACCTGGCCTTATTATTTTAACAGATTTTTAAATTTTAACATACCTACTTCCAGAAATAATTTTAGGCTTGGCTTGCAAGCCCCTTGAGTGGCTGGAGTTCAAGTGGTATTCACTGCTGGTTTTCTCCTAGTCCTTGACTCCCCAGTGGCCTGGCATGGGCGCTGTTGAGAGAGGGGCACTTTTGAAGTGGCCCGTGGAGCTCAAGGCAGGGCTGAACCCTCTGCCTGCTCCGCTTCAGGCCTCTGGCCCCTGGATGCTGAGCTGCTGCTGCTTCCTGTCAACACAGACTCTTCTGTGGATGCTACAGCAGCCAGACCTCCCTGGCACCCCCCACACCTAGAACGATATGTTCAGAACATAAAAGAATATAGTCATTAGTAGAGGTGAAAACAGGTTCTTAGAGTGAAGTGTGTTCCTCAGGAAATCAGCTTCACTCCCCAGCACCTGGCTTCCCTGGTTCTTTCTGGATGAAGAAAGACCTTTACCCTACACGTTGGAAGTATAGGTGAGCATCTCTTAATTAAAGCTACCATTTGAGAGGAATATAGCAAATCCTCAATACCTAACTAGCAGAACAGTGAGACTCTTTTGTGAAGTTCACACATGACCAGATGATGTGATGATACAGGGTAAGGCCAACAGGCCCTGTGCCTTGAAGCTTCTTTGCATATCGGTCCCTCCAGAGGTGGCTGCTGTACACTTTCCGCAACTGGTTTGCCATCGCATTTCAGCTCCAGCTGCATCTGAGAACACTCAAATGTCTCTTTAGGTCTTTTTAAAAAATTGTGATTAAAGATAACATAAAATGTATCATGTTAACTATTCTTATGTGTACAGTTCAGTAGTGTTAAATGTGTTCACATTGTTGTGAAACAGATCTCTAGAATTTTTCATCTTACAAACCTGAAACTCTGTCCCCATTTAACAACTCCGCCTTTATCCTCCCCCTAGGCCTTGGCAGCCACTATTCTACTTTCTGTCTATGAATTGGCTACTTTAGATATGTCATATAAATGGAATTATGCAGTATTCGTCTTTCTGTAATTGGCTTATTTCACTCAGCATAATGTCGTCAAAGTTCATTCATGTTGCAATGTATGACAAGATTTCCTTTCCTTTTAAAGGCTGAATAATAATCTGTGATATATATTCACAAACACATACACACACACACACACACACACCCCCACAGTTTATCTGTTCTTCTGTTGATGGACACTTGGGTTGCTTCCACCTCTTGGCTATTAAGAATAGTGCTGTTGG-A	Joubert syndrome 30	Uncertain significance (Jan 07, 2019)	636278
2-231206193-T-C		Benign (May 04, 2021)	1226717
2-231206246-A-G		Uncertain significance (Jan 10, 2025)	3672397
2-231206248-A-G	ARMC9-related disorder	Benign (Jan 15, 2025)	727719
2-231206251-C-A		Uncertain significance (Jan 16, 2022)	1962484
2-231206251-C-G	Inborn genetic diseases	Uncertain significance (Nov 18, 2024)	967189
2-231206254-G-C		Uncertain significance (Sep 06, 2022)	2105406
2-231206257-C-T		Uncertain significance (Feb 21, 2022)	1949383
2-231206263-T-C		Uncertain significance (Jan 24, 2022)	1700532
2-231206273-T-C		Uncertain significance (Sep 27, 2022)	1716787
2-231206294-G-T	Familial aplasia of the vermis • ARMC9-related Joubert syndrome • Joubert syndrome 30	Conflicting classifications of pathogenicity (Mar 25, 2024)	427931
2-231206296-A-G		Likely benign (Jun 16, 2024)	3607962
2-231206297-T-A		Likely benign (Feb 23, 2024)	1905042
2-231206304-C-G		Likely benign (Feb 24, 2024)	1912626
2-231206309-C-T		Likely benign (Nov 19, 2024)	1899300
2-231208109-A-C		Benign (Nov 28, 2024)	1168970
2-231208109-ATTAT-A		Likely benign (Feb 24, 2024)	2007025
2-231208116-A-T		Likely benign (Oct 01, 2021)	1606945
2-231208150-A-G		Likely benign (Nov 29, 2022)	2013108
2-231208151-G-C	Inborn genetic diseases	Uncertain significance (Jan 04, 2024)	2241680
2-231208175-G-T	Joubert syndrome 30	Pathogenic (Apr 20, 2018)	1034090
2-231208185-T-C		Uncertain significance (Aug 21, 2022)	1410572
2-231208199-T-C		Benign (Feb 03, 2025)	1167998
2-231208212-T-G		Uncertain significance (Oct 24, 2022)	1473481
2-231208216-C-T		Benign (Feb 03, 2025)	1170309

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMC9	protein_coding	protein_coding	ENST00000349938	20	176289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.20e-17	0.179	125663	0	85	125748	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.851	333	380	0.877	0.0000216	4355
Missense in Polyphen		106	139.74	0.75855		1576
Synonymous	0.188	150	153	0.981	0.00000912	1254
Loss of Function	1.29	30	38.6	0.776	0.00000182	483

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000784	0.000782
Ashkenazi Jewish	0.00	0.00
East Asian	0.000491	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000531	0.000378
Middle Eastern	0.000491	0.000489
South Asian	0.000462	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for ciliogenesis. {ECO:0000250|UniProtKB:E7F187}.;
Disease: DISEASE: 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. {ECO:0000269|PubMed:28625504}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.243

Intolerance Scores

loftool: 0.927
rvis_EVS: 0.25
rvis_percentile_EVS: 69.62

Haploinsufficiency Scores

pHI: 0.347
hipred: N
hipred_score: 0.348
ghis: 0.463

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.380

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Armc9
Phenotype

Zebrafish Information Network

Gene name: armc9
Affected structure: photoreceptor cell
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

Biological process: cilium assembly
Cellular component: cytoplasm;ciliary basal body;extracellular exosome
Molecular function