TTLL10

protein-coding

tubulin tyrosine ligase like 10, the group of Tubulin tyrosine ligase family

Gene summary

Predicted to enable protein-glycine ligase activity, elongating. Predicted to be involved in protein polyglycylation. Predicted to be located in axoneme and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TTLL5

MANE transcript

NM_001130045.2

Inheritance

—

ClinVar variants

U:158B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr1:1,173,880-1,197,936

External References & Databases

Ensembl (ENSG00000162571)

Transcript & Mutation Effects

hg38 • Region Span ~24.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TTLL10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 167

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130045.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			153 clinvar	18 clinvar		171
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	158	19	0	177

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130045.2	RefSeq	NP_001123517.1	13	MANE Select
ENST00000379289.6	Ensembl	ENSP00000368591.1	13	MANE Select
NM_001371649.1	RefSeq	NP_001358578.1	13	Standard
NM_153254.3	RefSeq	NP_694986.2	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
Carboxyterminal post-translational modifications of tubulin

Biological Process

protein polyglycylation

Molecular Function

protein binding
ATP binding
protein-glycine ligase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379290
Coding exons: 13
Length: 24052
Individuals with no LoFs: 125180
Homozygous LoFs: 5
Heterozygous LoFs: 562
Defined: 125747
p: 0.00226

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.330	387	406	0.954	0.0000271	4295
Missense (PolyPhen)		109	118.78	0.91763		1414
Synonymous	0.452	167	175	0.956	0.0000126	1367
Loss of Function	1.04	20	25.7	0.779	0.00000124	293

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0070	0.0064	notable
Latino/Admixed American	0.00077	0.00072	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.021	0.019	notable
Finnish	0.00027	0.00023	rare
European (Non-Finnish)	0.00063	0.00050	rare
South Asian	0.00024	0.00023	rare
Other	0.0028	0.0026	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inactive polyglycylase. {ECO:0000269|PubMed:19524510}.;

Intolerance Scores

LoFtool: 0.950
RVIS EVS: 3.27
RVIS percentile EVS: 99.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0885

Gene Damage Prediction

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