TPPP

tubulin polymerization promoting protein, the group of Tubulin polymerization promoting proteins

Basic information

Region (hg38): 5:659862-693352

Links

ENSG00000171368 ∙ NCBI:11076 ∙ OMIM:608773 ∙ HGNC:24164 ∙ Uniprot:O94811 ∙ 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 TPPP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPPP 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				5	3	8
missense			14		1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				4		4
Total	0	0	14	9	4

Variants in TPPP

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

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

Position	Type	Phenotype	Significance	ClinVar
5-665113-C-T		not specified	Uncertain significance (Apr 20, 2023)
5-665129-G-A			Likely benign (Jun 17, 2018)
5-665141-G-A			Benign (Dec 31, 2019)
5-665159-A-G			Likely benign (Jun 04, 2018)
5-665160-T-C		not specified	Uncertain significance (May 31, 2023)
5-665170-C-T		not specified	Uncertain significance (Feb 21, 2024)
5-665199-C-A		not specified	Uncertain significance (Feb 28, 2024)
5-665243-C-T			Likely benign (Nov 27, 2017)
5-665261-C-T			Benign (Dec 31, 2019)
5-665262-G-A		not specified	Uncertain significance (Nov 16, 2021)
5-665296-T-C		not specified	Uncertain significance (Apr 08, 2022)
5-665991-C-T			Likely benign (Mar 01, 2023)
5-666022-C-T		not specified	Uncertain significance (Jun 23, 2021)
5-666035-C-T		not specified	Uncertain significance (Aug 30, 2022)
5-666040-C-T		not specified	Uncertain significance (Feb 22, 2023)
5-666065-C-T		not specified	Uncertain significance (Mar 31, 2023)
5-666079-G-C		not specified	Uncertain significance (Jan 31, 2024)
5-666129-G-GGGGCACAGGCGACTTA			Benign (Jan 18, 2024)
5-666129-G-GGGGCACAGGCAGTCGACTTA			Likely benign (Dec 31, 2019)
5-668046-G-C			Likely benign (Jan 01, 2023)
5-668207-C-G			Likely benign (Jul 01, 2023)
5-668207-CGACAAGCACACAGAGAGGGGGCCGTGTGGGCGCCGTCAGGGAAGTGCG-C			Likely benign (Dec 01, 2022)
5-668315-A-G			Likely benign (Jan 01, 2023)
5-677743-C-A			Likely benign (Sep 12, 2018)
5-677766-C-T		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPPP	protein_coding	protein_coding	ENST00000360578	3	32628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.203	0.758	125524	0	9	125533	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	122	148	0.824	0.0000101	1402
Missense in Polyphen		32	54.776	0.5842		527
Synonymous	-0.995	82	71.3	1.15	0.00000581	443
Loss of Function	1.72	2	6.85	0.292	3.72e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000883	0.00000882
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the polymerization of tubulin into microtubules, microtubule bundling and the stabilization of existing microtubules, thus maintaining the integrity of the microtubule network. May play a role in mitotic spindle assembly and nuclear envelope breakdown. {ECO:0000269|PubMed:17105200, ECO:0000269|PubMed:17693641, ECO:0000269|PubMed:18028908}.
• Pathway: Regulation of Microtubule Cytoskeleton;Glial Cell Differentiation;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.359
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.328
• hipred: Y
• hipred_score: 0.559
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tppp
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: microtubule bundle formation;positive regulation of protein complex assembly;positive regulation of protein polymerization;microtubule polymerization
• Cellular component: nucleus;cytoplasm;mitochondrion;cytosol;microtubule;myelin sheath;perinuclear region of cytoplasm;microtubule bundle
• Molecular function: protein binding;microtubule binding;tubulin binding