TTLL1

TTL family tubulin polyglutamylase complex subunit L1, the group of Tubulin polyglutamylase complex subunits|Tubulin tyrosine ligase family

Basic information

Region (hg38): 22:43039516-43089419

Previous symbols: [ "C22orf7" ]

Links

ENSG00000100271 ∙ NCBI:25809 ∙ OMIM:608955 ∙ HGNC:1312 ∙ Uniprot:O95922 ∙ 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 TTLL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTLL1 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	3
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	15	0	4

Variants in TTLL1

This is a list of pathogenic ClinVar variants found in the TTLL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43039806-C-T		not specified	Benign (Mar 29, 2016)
22-43039819-C-T		not specified	Uncertain significance (Dec 17, 2021)
22-43039856-T-C		not specified	Uncertain significance (May 06, 2022)
22-43046471-T-C		not specified	Uncertain significance (Apr 07, 2022)
22-43046482-G-A		not specified	Uncertain significance (Nov 30, 2022)
22-43046551-G-A		not specified	Uncertain significance (May 26, 2022)
22-43051885-C-T		not specified	Benign (Mar 29, 2016)
22-43059426-G-A		not specified	Benign (Mar 29, 2016)
22-43059451-T-C			Benign (Apr 20, 2018)
22-43059457-C-T		not specified	Uncertain significance (Nov 09, 2023)
22-43059508-T-C		not specified	Uncertain significance (Aug 04, 2021)
22-43059525-C-T		not specified	Benign (Mar 29, 2016)
22-43063838-G-C		not specified	Uncertain significance (Feb 16, 2023)
22-43063840-G-A		not specified	Benign (Mar 29, 2016)
22-43063848-C-T		not specified	Uncertain significance (Apr 05, 2023)
22-43063853-A-G		not specified	Uncertain significance (Jul 05, 2023)
22-43063890-C-T		not specified	Uncertain significance (Jun 28, 2022)
22-43063902-G-A		not specified	Uncertain significance (Oct 06, 2023)
22-43064209-G-A		not specified	Uncertain significance (Jan 10, 2023)
22-43064243-G-T		not specified	Uncertain significance (Aug 16, 2021)
22-43064251-T-C		not specified	Uncertain significance (Apr 26, 2023)
22-43069665-T-C		not specified	Uncertain significance (Jun 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTLL1	protein_coding	protein_coding	ENST00000266254	9	49913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000591	0.973	125702	0	45	125747	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	194	260	0.745	0.0000166	2778
Missense in Polyphen		56	90.334	0.61992		1004
Synonymous	-0.658	118	109	1.08	0.00000767	785
Loss of Function	2.03	12	22.3	0.537	0.00000120	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.000273	0.000272
South Asian	0.0000980	0.0000980
Other	0.000385	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the neuronal tubulin polyglutamylase complex. Modifies alpha- and beta-tubulin, generating side chains of glutamate on the gamma-carboxyl groups of specific glutamate residues within the C-terminal tail of alpha- and beta-tubulin (By similarity). {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.804
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.192
• hipred: Y
• hipred_score: 0.639
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.529

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttll1
• Phenotype: hearing/vestibular/ear phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; growth/size/body region phenotype; reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: epithelial cilium movement;sperm axoneme assembly;protein polyglutamylation;sperm flagellum movement involved in flagellated sperm motility
• Cellular component: cytoplasm;microtubule
• Molecular function: ATP binding;tubulin-glutamic acid ligase activity