TPGS1

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

Basic information

Region (hg38): 19:507497-519654

Previous symbols: [ "C19orf20" ]

Links

ENSG00000141933 ∙ NCBI:91978 ∙ ∙ HGNC:25058 ∙ Uniprot:Q6ZTW0 ∙ 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 TPGS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPGS1 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				2	3	5
missense			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	4	3

Variants in TPGS1

This is a list of pathogenic ClinVar variants found in the TPGS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-507513-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-507545-G-A			Benign (Apr 09, 2018)
19-507550-C-A		not specified	Uncertain significance (Apr 23, 2024)
19-507597-G-A		not specified	Likely benign (Jul 14, 2021)
19-507611-G-C		not specified	Uncertain significance (Mar 11, 2022)
19-507625-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-507641-G-A			Likely benign (Dec 31, 2019)
19-507651-C-T		not specified	Uncertain significance (Jun 12, 2023)
19-507655-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-507705-C-G		not specified	Uncertain significance (Jan 23, 2024)
19-507766-C-T		not specified	Uncertain significance (Mar 23, 2022)
19-507787-A-G		not specified	Uncertain significance (Dec 06, 2023)
19-518893-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-518896-T-A		not specified	Uncertain significance (Jun 28, 2023)
19-518900-A-G		not specified	Uncertain significance (Feb 03, 2022)
19-518914-G-T		not specified	Uncertain significance (Aug 02, 2021)
19-518921-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-518945-G-C		not specified	Uncertain significance (Nov 22, 2021)
19-518967-C-G		not specified	Uncertain significance (May 15, 2023)
19-518982-C-T			Benign (May 14, 2018)
19-518995-C-A		not specified	Uncertain significance (Oct 17, 2023)
19-519064-G-C		not specified	Uncertain significance (Sep 15, 2021)
19-519098-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-519103-A-G		not specified	Uncertain significance (May 31, 2024)
19-519194-G-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPGS1	protein_coding	protein_coding	ENST00000359315	2	12356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0616	0.736	105595	0	11	105606	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	62	99.4	0.624	0.00000664	1747
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00100	0.000986
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000110	0.0000105
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000192	0.000189

dbNSFP

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}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.272
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpgs1
• Phenotype: cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); reproductive system phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: chemical synaptic transmission;multicellular organism development;sperm axoneme assembly;protein polyglutamylation;adult behavior;vesicle localization
• Cellular component: cytoplasm;centrosome;microtubule;axon;dendrite;motile cilium
• Molecular function: microtubule binding;tubulin-glutamic acid ligase activity