TTLL2

tubulin tyrosine ligase like 2, the group of Tubulin tyrosine ligase family

Basic information

Region (hg38): 6:167325071-167359503

Previous symbols: [ "C6orf104" ]

Links

ENSG00000120440 ∙ NCBI:83887 ∙ ∙ HGNC:21211 ∙ Uniprot:Q9BWV7 ∙ 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 TTLL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTLL2 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			34	6	2	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	6	2

Variants in TTLL2

This is a list of pathogenic ClinVar variants found in the TTLL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-167325184-G-A		not specified	Uncertain significance (Mar 17, 2023)
6-167338705-A-G		not specified	Uncertain significance (Feb 15, 2023)
6-167338711-C-G		not specified	Uncertain significance (Dec 15, 2023)
6-167340121-T-C		not specified	Uncertain significance (May 16, 2023)
6-167340168-C-T		not specified	Uncertain significance (Dec 27, 2023)
6-167340183-A-T		not specified	Uncertain significance (May 16, 2024)
6-167340213-G-A		not specified	Uncertain significance (May 28, 2023)
6-167340252-G-A		not specified	Uncertain significance (Jun 30, 2022)
6-167340286-C-T		not specified	Uncertain significance (Nov 02, 2023)
6-167340319-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-167340386-C-A		not specified	Uncertain significance (Sep 23, 2023)
6-167340408-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-167340447-G-A		not specified	Likely benign (Apr 11, 2023)
6-167340478-C-T		not specified	Uncertain significance (Jul 05, 2022)
6-167340503-G-A		not specified	Uncertain significance (Nov 02, 2023)
6-167340505-T-C			Benign (Dec 31, 2019)
6-167340552-C-T		not specified	Uncertain significance (Jan 24, 2024)
6-167340607-T-C		not specified	Likely benign (Sep 29, 2022)
6-167340639-T-G		not specified	Uncertain significance (Feb 06, 2024)
6-167340670-G-A		not specified	Uncertain significance (Nov 12, 2021)
6-167340670-G-C		not specified	Uncertain significance (Dec 19, 2022)
6-167340721-A-C		not specified	Uncertain significance (Sep 17, 2021)
6-167340759-C-G		not specified	Uncertain significance (Dec 17, 2023)
6-167340778-A-G		not specified	Uncertain significance (Jul 06, 2021)
6-167340816-G-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTLL2	protein_coding	protein_coding	ENST00000239587	3	34418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00585	0.507	125054	0	2	125056	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.189	320	330	0.971	0.0000185	3905
Missense in Polyphen		91	89.255	1.0196		1192
Synonymous	-0.331	138	133	1.04	0.00000805	1147
Loss of Function	-0.0845	3	2.85	1.05	1.21e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000105	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable tubulin polyglutamylase that forms polyglutamate side chains on tubulin. Probably acts when complexed with other proteins (By similarity). {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Intolerance Scores

• loftool: 0.880
• rvis_EVS: 1.59
• rvis_percentile_EVS: 95.81

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0711

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttll2

Gene ontology

• Biological process: cellular protein modification process
• Molecular function: ATP binding;ligase activity