TPGS1

protein-coding

tubulin polyglutamylase complex subunit 1, the group of Tubulin polyglutamylase complex subunits

Gene summary

Predicted to enable microtubule binding activity and tubulin-glutamic acid ligase activity. Predicted to be involved in sperm axoneme assembly. Predicted to act upstream of or within several processes, including adult behavior; chemical synaptic transmission; and protein polyglutamylation. Located in centrosome. [provided by Alliance of Genome Resources, Apr 2025]

Previous symbols:

C19orf20

MANE transcript

NM_033513.3

Inheritance

—

ClinVar variants

U:78B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr19:507,497-519,654

External References & Databases

Ensembl (ENSG00000141933)

Transcript & Mutation Effects

hg38 • Region Span ~12.2 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 TPGS1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033513.3. 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	2 clinvar	4
missense			78 clinvar	2 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	4	2	84

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033513.3	RefSeq	NP_277048.2	2	MANE Select
ENST00000359315.6	Ensembl	ENSP00000352265.4	2	MANE Select
ENST00001120855.1	Ensembl	ENSP00000790660.1	2	Standard
ENST00001120856.1	Ensembl	ENSP00000790661.1	2	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

chemical synaptic transmission
multicellular organism development
sperm axoneme assembly
protein polyglutamylation
adult behavior

Molecular Function

microtubule binding
tubulin-glutamic acid ligase activity

Cellular Component

cytoplasm
centrosome
microtubule
axon
dendrite

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359315
Coding exons: 2
Length: 12356
Individuals with no LoFs: 105595
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 105606
p: 0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.33	62	99.4	0.624	0.00000664	1747
Missense (PolyPhen)		14	31.303	0.44724		598
Synonymous	0.631	43	48.6	0.885	0.00000344	652
Loss of Function	0.832	2	3.74	0.535	1.62e-7	62

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.0010	0.00099	notable
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000011	0.000011	rare
South Asian	0	0.0	absent
Other	0.00019	0.00019	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act in the targeting of the tubulin polyglutamylase complex. Required for the development of the spermatid flagellum (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.109

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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