TOGARAM1

TOG array regulator of axonemal microtubules 1, the group of TOG domain containing

Basic information

Region (hg38): 14:44962190-45074431

Previous symbols: [ "KIAA0423", "FAM179B" ]

Links

ENSG00000198718 ∙ NCBI:23116 ∙ OMIM:617618 ∙ HGNC:19959 ∙ Uniprot:Q9Y4F4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliopathy (Limited), mode of inheritance: AR
• Joubert syndrome 37 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 37	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Renal	32453716; 32747439
The condition may involve multi-systemic manifestations, including sequelae affecting the renal and hepatic systems, and surveillance and avoidance of certain medications (eg, nephrotoxic agents) may be beneficial

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TOGARAM1 gene.

• Familial aplasia of the vermis (5 variants)
• Joubert syndrome 37 (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOGARAM1 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				10	1	11
missense	2		83	4		89
nonsense	3	2				5
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region		1	1	1		3
non coding						0
Total	5	3	85	14	1

Variants in TOGARAM1

This is a list of pathogenic ClinVar variants found in the TOGARAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-44962429-C-T		not specified	Uncertain significance (Feb 17, 2024)
14-44962430-T-C			Likely benign (Jun 01, 2024)
14-44962445-G-A			Likely benign (Dec 01, 2023)
14-44962453-T-C		not specified	Uncertain significance (Oct 25, 2023)
14-44962455-C-T		not specified	Uncertain significance (Sep 28, 2022)
14-44962480-A-G		not specified	Uncertain significance (Nov 21, 2022)
14-44962495-G-A		not specified	Uncertain significance (Sep 26, 2023)
14-44962504-C-G		not specified	Uncertain significance (Nov 12, 2021)
14-44962508-CG-T			Uncertain significance (May 01, 2024)
14-44962518-A-G		not specified	Uncertain significance (Sep 26, 2023)
14-44962567-A-G		not specified	Likely benign (May 26, 2023)
14-44962570-T-G		not specified	Likely benign (Aug 11, 2022)
14-44962726-T-A		not specified	Uncertain significance (Dec 28, 2023)
14-44962735-C-A		not specified	Uncertain significance (Apr 29, 2023)
14-44962756-C-G		not specified	Uncertain significance (May 10, 2024)
14-44962762-A-G		not specified	Uncertain significance (Jul 17, 2023)
14-44962785-C-T		not specified	Uncertain significance (Nov 21, 2022)
14-44962815-C-G		not specified	Uncertain significance (Aug 04, 2023)
14-44963023-A-T		not specified	Uncertain significance (Oct 27, 2023)
14-44963077-T-C		not specified	Uncertain significance (Oct 13, 2023)
14-44963165-G-A			Likely benign (Jul 01, 2022)
14-44963196-T-C		not specified	Uncertain significance (Aug 02, 2023)
14-44963203-C-G		not specified	Uncertain significance (Jan 18, 2023)
14-44963263-A-G		not specified	Uncertain significance (Mar 07, 2024)
14-44963320-C-T		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOGARAM1	protein_coding	protein_coding	ENST00000361577	19	112224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-8	1.00	125652	0	96	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.607	835	886	0.943	0.0000426	11140
Missense in Polyphen		232	277	0.83755		3559
Synonymous	0.632	314	329	0.956	0.0000157	3501
Loss of Function	4.92	27	72.1	0.374	0.00000401	913

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000701	0.000699
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000328	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000417	0.000413
Middle Eastern	0.000328	0.000326
South Asian	0.000464	0.000457
Other	0.00117	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal structure and function of primary cilia. Plays a role in the organization of axoneme microtubule bundles in primary cilia (By similarity). Interacts with microtubules and promotes microtubule polymerization via its HEAT repeat domains, especially those in TOG region 2 and 4 (By similarity). {ECO:0000250|UniProtKB:Q17423, ECO:0000250|UniProtKB:Q6A070}.

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.97

Haploinsufficiency Scores

• pHI: 0.411
• hipred: N
• hipred_score: 0.372
• ghis: 0.619

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Togaram1

Gene ontology

• Biological process: positive regulation of microtubule polymerization;axoneme assembly;non-motile cilium assembly
• Cellular component: cytoplasm;microtubule;cilium;ciliary basal body