TPPP3

protein-coding

tubulin polymerization promoting protein family member 3, the group of Tubulin polymerization promoting proteins

Gene summary

Enables tubulin binding activity. Involved in decidualization and microtubule bundle formation. Located in microtubule bundle and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015964.4

Inheritance

—

ClinVar variants

U:23

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr16:67,389,809-67,393,518

External References & Databases

Ensembl (ENSG00000159713)

Transcript & Mutation Effects

hg38 • Region Span ~3.7 kb

Loading mutation effect viewer...

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 TPPP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015964.4. 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
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	0	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015964.4	RefSeq	NP_057048.2	3	MANE Select
ENST00000393957.7	Ensembl	ENSP00000377529.2	3	MANE Select
NM_016140.4	RefSeq	NP_057224.2	3	Standard
ENST00000290942.10	Ensembl	ENSP00000290942.5	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

Biological Process

microtubule bundle formation
positive regulation of protein polymerization
microtubule polymerization

Molecular Function

tubulin binding

Cellular Component

microtubule
perinuclear region of cytoplasm
microtubule bundle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000564104
Coding exons: 3
Length: 3727
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125746
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.878	89	116	0.770	0.00000719	1162
Missense (PolyPhen)		36	52.776	0.68213		501
Synonymous	0.744	42	48.6	0.864	0.00000334	336
Loss of Function	1.60	1	4.76	0.210	1.97e-7	73

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds tubulin and has microtubule bundling activity. May play a role in cell proliferation and mitosis. {ECO:0000269|PubMed:17105200, ECO:0000269|PubMed:19633818}.;

Intolerance Scores

LoFtool: 0.625
RVIS EVS: -0.14
RVIS percentile EVS: 43.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0759

Gene Damage Prediction

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