TTLL6

tubulin tyrosine ligase like 6, the group of Tubulin tyrosine ligase family

Basic information

Region (hg38): 17:48762233-48817229

Links

ENSG00000170703 ∙ NCBI:284076 ∙ OMIM:610849 ∙ HGNC:26664 ∙ Uniprot:Q8N841 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TTLL6 gene.

• Inborn genetic diseases (43 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTLL6 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						0
missense			32	11	1	44
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	11	2

Variants in TTLL6

This is a list of pathogenic ClinVar variants found in the TTLL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48769035-T-C		not specified	Uncertain significance (Dec 14, 2021)
17-48769087-T-C		not specified	Uncertain significance (Dec 21, 2022)
17-48769132-G-T		not specified	Uncertain significance (Jan 03, 2022)
17-48769222-G-A		not specified	Likely benign (Feb 23, 2023)
17-48769745-C-A		not specified	Likely benign (May 03, 2023)
17-48769793-A-T		not specified	Uncertain significance (May 11, 2022)
17-48769815-C-T		not specified	Uncertain significance (Aug 26, 2022)
17-48769825-A-C		not specified	Uncertain significance (May 06, 2022)
17-48769886-C-T		not specified	Uncertain significance (Mar 16, 2022)
17-48769974-C-T		not specified	Uncertain significance (Jan 09, 2024)
17-48769985-G-A		not specified	Likely benign (Dec 14, 2021)
17-48770002-C-A			Benign (Jul 13, 2018)
17-48770013-C-T		not specified	Likely benign (Feb 10, 2022)
17-48770033-G-A		not specified	Likely benign (Jun 11, 2021)
17-48770054-A-G		not specified	Uncertain significance (Jan 29, 2024)
17-48770055-G-C		not specified	Likely benign (Aug 12, 2021)
17-48770085-C-A		not specified	Uncertain significance (Jan 23, 2024)
17-48784940-C-T		not specified	Likely benign (Nov 09, 2022)
17-48785035-G-A		not specified	Uncertain significance (May 18, 2023)
17-48785036-G-T		not specified	Uncertain significance (Oct 29, 2021)
17-48785095-G-A		not specified	Likely benign (Jan 02, 2024)
17-48785137-C-T		not specified	Likely benign (Sep 26, 2023)
17-48786171-G-T		not specified	Uncertain significance (Aug 02, 2021)
17-48786174-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-48786247-C-T		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTLL6	protein_coding	protein_coding	ENST00000393382	15	54980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.77e-20	0.0582	125210	4	533	125747	0.00214

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	426	489	0.871	0.0000266	5902
Missense in Polyphen		107	147.84	0.72373		1831
Synonymous	0.0941	195	197	0.991	0.0000113	1653
Loss of Function	1.15	34	42.0	0.809	0.00000206	514

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00229	0.00229
Ashkenazi Jewish	0.000994	0.000993
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00156	0.00156
Middle Eastern	0.000217	0.000217
South Asian	0.00885	0.00876
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polyglutamylase which preferentially modifies alpha- tubulin. Mediates tubulin polyglutamylation in cilia. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation step. Generates long side-chains. Generates polyglutamylation of CGAS, leading to impair the DNA- binding activity of CGAS. {ECO:0000250|UniProtKB:A4Q9E8}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Intolerance Scores

• loftool: 0.931
• rvis_EVS: -0.13
• rvis_percentile_EVS: 44.03

Haploinsufficiency Scores

• pHI: 0.0595
• hipred: N
• hipred_score: 0.153
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttll6
• Phenotype: homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: ttll6
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: microtubule bundle formation;positive regulation of cilium movement;protein polyglutamylation;microtubule severing
• Cellular component: cytosol;microtubule;ciliary basal body
• Molecular function: protein binding;ATP binding;tubulin binding;protein-glutamic acid ligase activity;tubulin-glutamic acid ligase activity