TTBK1

tau tubulin kinase 1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 6:43243481-43288258

Links

ENSG00000146216 ∙ NCBI:84630 ∙ OMIM:619415 ∙ HGNC:19140 ∙ Uniprot:Q5TCY1 ∙ 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 TTBK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTBK1 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				3	4	7
missense		1	80	9	3	93
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding						0
Total	0	1	81	12	7

Variants in TTBK1

This is a list of pathogenic ClinVar variants found in the TTBK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43246688-G-C		not specified	Uncertain significance (Nov 07, 2022)
6-43246691-G-A		not specified	Uncertain significance (Dec 13, 2022)
6-43252781-G-T		not specified	Uncertain significance (Apr 20, 2024)
6-43252789-C-G		not specified	Uncertain significance (Jan 17, 2023)
6-43252821-T-C		not specified	Uncertain significance (Dec 19, 2022)
6-43253314-A-G		not specified	Uncertain significance (Oct 21, 2021)
6-43253565-C-T		not specified	Uncertain significance (May 12, 2015)
6-43253604-C-T		6 conditions	Uncertain significance (May 17, 2023)
6-43254624-C-T			Benign (May 18, 2018)
6-43254651-C-T			Likely benign (Nov 01, 2022)
6-43255101-C-T		not specified	Uncertain significance (Dec 20, 2021)
6-43255112-C-T		not specified	Uncertain significance (Mar 24, 2023)
6-43255645-G-T		Neurodevelopmental abnormality	Likely benign (Sep 03, 2020)
6-43255768-G-A		Childhood-onset schizophrenia	Likely pathogenic (Jan 01, 2014)
6-43257896-G-A		not specified	Uncertain significance (Mar 24, 2023)
6-43257906-T-C		not specified	Uncertain significance (Jan 08, 2024)
6-43257927-C-G		not specified	Uncertain significance (Mar 20, 2024)
6-43259125-G-A			Likely benign (Mar 01, 2022)
6-43259192-C-A		not specified	Uncertain significance (Sep 14, 2023)
6-43259198-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-43259264-G-A		not specified	Uncertain significance (May 27, 2022)
6-43259559-G-A		not specified	Uncertain significance (Aug 17, 2021)
6-43259597-C-G		not specified	Uncertain significance (Aug 02, 2022)
6-43259636-C-T		not specified	Uncertain significance (Oct 12, 2021)
6-43259637-G-A		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTBK1	protein_coding	protein_coding	ENST00000259750	14	44580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000333	125674	0	8	125682	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	555	759	0.731	0.0000497	8269
Missense in Polyphen		199	363.52	0.54742		3816
Synonymous	0.169	335	339	0.988	0.0000230	2878
Loss of Function	5.53	5	45.0	0.111	0.00000259	522

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000607	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000183	0.0000176
Middle Eastern	0.0000607	0.0000544
South Asian	0.0000363	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine kinase which is able to phosphorylate TAU on serine, threonine and tyrosine residues. Induces aggregation of TAU. {ECO:0000269|PubMed:16923168}.
• Pathway: Ras Signaling (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.276
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.69

Haploinsufficiency Scores

• pHI: 0.267
• hipred: Y
• hipred_score: 0.774
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.697

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttbk1

Gene ontology

• Biological process: protein phosphorylation;learning or memory;positive regulation of gene expression;negative regulation of gene expression;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;peptidyl-tyrosine phosphorylation;substantia nigra development;negative regulation of protein binding;positive regulation of protein polymerization;positive regulation of astrocyte activation;positive regulation of microglial cell activation;positive regulation of cyclin-dependent protein kinase activity;positive regulation of cysteine-type endopeptidase activity
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;microtubule associated complex;neuronal cell body;perinuclear region of cytoplasm
• Molecular function: protein serine/threonine kinase activity;ATP binding;tau protein binding;tau-protein kinase activity