TTLL12

tubulin tyrosine ligase like 12, the group of Tubulin tyrosine ligase family

Basic information

Region (hg38): 22:43166622-43187134

Links

ENSG00000100304 ∙ NCBI:23170 ∙ OMIM:619410 ∙ HGNC:28974 ∙ Uniprot:Q14166 ∙ 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 TTLL12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTLL12 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				6	4	10
missense			74	8		82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	74	14	4

Variants in TTLL12

This is a list of pathogenic ClinVar variants found in the TTLL12 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43168025-C-T		not specified	Uncertain significance (May 14, 2024)
22-43168028-G-A		not specified	Uncertain significance (Jan 24, 2025)
22-43168089-G-A			Likely benign (Oct 16, 2017)
22-43168102-C-T		not specified	Uncertain significance (Dec 07, 2024)
22-43168148-T-C		not specified	Uncertain significance (Oct 17, 2023)
22-43168783-C-G		not specified	Likely benign (Oct 10, 2023)
22-43168783-C-T		not specified	Uncertain significance (Sep 04, 2024)
22-43168784-G-T		not specified	Uncertain significance (Oct 10, 2023)
22-43168801-T-C		not specified	Uncertain significance (May 02, 2024)
22-43168808-G-A			Benign (Jun 07, 2017)
22-43168880-G-T		not specified	Uncertain significance (Nov 16, 2021)
22-43168899-C-T		not specified	Likely benign (Jan 10, 2022)
22-43168906-T-C		not specified	Uncertain significance (Aug 04, 2024)
22-43168917-G-T			Benign (Jul 13, 2018)
22-43169510-G-A		not specified	Uncertain significance (Dec 30, 2024)
22-43169518-A-C		not specified	Uncertain significance (Oct 05, 2023)
22-43169543-T-A		not specified	Uncertain significance (Jan 27, 2022)
22-43169544-C-T		not specified	Uncertain significance (Dec 28, 2023)
22-43171835-T-C		not specified	Uncertain significance (Apr 18, 2023)
22-43171854-C-T		not specified	Uncertain significance (Sep 25, 2024)
22-43171855-C-T			Benign (Jul 13, 2018)
22-43171885-G-C		not specified	Uncertain significance (Jul 09, 2021)
22-43172437-C-T		not specified	Uncertain significance (May 13, 2022)
22-43172461-A-T		not specified	Uncertain significance (Apr 08, 2024)
22-43172473-C-T		not specified	Uncertain significance (Jan 02, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTLL12	protein_coding	protein_coding	ENST00000216129	14	20512

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-15	0.205	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.813	440	395	1.12	0.0000265	4179
Missense in Polyphen		128	122.72	1.043		1227
Synonymous	-1.15	191	172	1.11	0.0000129	1223
Loss of Function	1.21	27	34.7	0.779	0.00000188	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000647	0.000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000407	0.000360
Middle Eastern	0.000163	0.000163
South Asian	0.000409	0.000392
Other	0.000339	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.881
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.7

Haploinsufficiency Scores

• pHI: 0.506
• hipred: N
• hipred_score: 0.251
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttll12

Gene ontology

• Biological process: cellular protein modification process
• Molecular function: ATP binding