TPPP3

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

Basic information

Region (hg38): 16:67389809-67393518

Links

ENSG00000159713 ∙ NCBI:51673 ∙ OMIM:616957 ∙ HGNC:24162 ∙ Uniprot:Q9BW30 ∙ 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 TPPP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPPP3 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						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in TPPP3

This is a list of pathogenic ClinVar variants found in the TPPP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67390259-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-67390334-C-T		not specified	Uncertain significance (Mar 16, 2024)
16-67390343-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-67390484-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-67390619-G-A		not specified	Uncertain significance (Dec 13, 2023)
16-67390987-C-G		not specified	Uncertain significance (Apr 09, 2024)
16-67391006-C-T		not specified	Uncertain significance (Jun 10, 2022)
16-67391048-C-T		not specified	Uncertain significance (Jul 15, 2021)
16-67391068-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPPP3	protein_coding	protein_coding	ENST00000564104	3	3727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.373	0.584	125718	0	28	125746	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.878	89	116	0.770	0.00000719	1162
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000873	0.000873
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

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}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Intolerance Scores

• loftool: 0.625
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.424
• hipred: Y
• hipred_score: 0.579
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0759

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tppp3

Gene ontology

• Biological process: microtubule bundle formation;positive regulation of protein polymerization;microtubule polymerization
• Cellular component: microtubule;perinuclear region of cytoplasm;microtubule bundle
• Molecular function: tubulin binding