TTLL3

tubulin tyrosine ligase like 3, the group of Tubulin tyrosine ligase family

Basic information

Region (hg38): 3:9808086-9855138

Links

ENSG00000214021 ∙ NCBI:26140 ∙ OMIM:619195 ∙ HGNC:24483 ∙ Uniprot:Q9Y4R7 ∙ 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 TTLL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTLL3 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			68	2		70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding			16			16
Total	0	0	84	2	0

Variants in TTLL3

This is a list of pathogenic ClinVar variants found in the TTLL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9810077-C-A		not specified	Uncertain significance (Dec 21, 2022)
3-9810110-A-C		not specified	Uncertain significance (Dec 14, 2023)
3-9810116-T-C		not specified	Likely benign (Oct 08, 2024)
3-9810124-C-G		not specified	Uncertain significance (Nov 21, 2022)
3-9810125-C-A		not specified	Uncertain significance (Nov 21, 2022)
3-9810136-G-A		not specified	Uncertain significance (Jun 12, 2023)
3-9810143-G-A		not specified	Uncertain significance (Jun 07, 2024)
3-9810179-G-T		not specified	Uncertain significance (May 20, 2024)
3-9810191-G-A		not specified	Uncertain significance (Oct 05, 2023)
3-9810244-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-9810245-G-T		not specified	Uncertain significance (Jan 23, 2024)
3-9810266-C-G		not specified	Uncertain significance (Aug 27, 2024)
3-9810268-G-A		not specified	Uncertain significance (Dec 06, 2022)
3-9810283-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-9810302-C-T		not specified	Uncertain significance (Aug 26, 2022)
3-9810331-G-A		not specified	Uncertain significance (May 14, 2024)
3-9810347-C-T		not specified	Uncertain significance (Feb 05, 2024)
3-9810349-C-T		not specified	Uncertain significance (Mar 17, 2023)
3-9810352-G-A		not specified	Uncertain significance (Jan 16, 2024)
3-9810356-C-G		not specified	Uncertain significance (Jul 02, 2024)
3-9810359-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-9810642-G-A		not specified	Uncertain significance (May 03, 2023)
3-9810701-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-9812983-T-C		not specified	Uncertain significance (Apr 26, 2023)
3-9812985-C-T		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTLL3	protein_coding	protein_coding	ENST00000426895	13	47053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-19	0.00879	116676	266	8806	125748	0.0367

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0565	510	506	1.01	0.0000302	5904
Missense in Polyphen		142	131.75	1.0778		1515
Synonymous	0.593	196	207	0.948	0.0000123	1881
Loss of Function	0.495	31	34.1	0.909	0.00000175	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0239	0.0235
Ashkenazi Jewish	0.0673	0.0662
East Asian	0.000971	0.000925
Finnish	0.0326	0.0324
European (Non-Finnish)	0.0418	0.0410
Middle Eastern	0.000971	0.000925
South Asian	0.0784	0.0779
Other	0.0363	0.0350

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Monoglycylase which modifies alpha- and beta-tubulin, generating side chains of glycine on the gamma-carboxyl groups of specific glutamate residues within the C-terminal tail of alpha- and beta-tubulin. Involved in the side-chain initiation step of the glycylation reaction by adding a single glycine chain to generate monoglycine side chains. Not involved in elongation step of the polyglycylation reaction. {ECO:0000269|PubMed:19524510}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.952
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttll3
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; normal phenotype; neoplasm; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: ttll3
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: protein polyglycylation;axoneme assembly;cilium assembly
• Cellular component: cytosol;microtubule;cilium;axoneme;microtubule cytoskeleton
• Molecular function: ATP binding;protein-glycine ligase activity;protein-glycine ligase activity, initiating