TPGS2

tubulin polyglutamylase complex subunit 2, the group of Tubulin polyglutamylase complex subunits

Basic information

Region (hg38): 18:36777647-36829216

Previous symbols: [ "C18orf10" ]

Links

ENSG00000134779 ∙ NCBI:25941 ∙ ∙ HGNC:24561 ∙ Uniprot:Q68CL5 ∙ 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 TPGS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPGS2 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				1		1
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in TPGS2

This is a list of pathogenic ClinVar variants found in the TPGS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-36779447-G-A		Cardiomyopathy, familial hypertrophic, 28	Likely pathogenic (Mar 29, 2024)
18-36779486-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
18-36779513-T-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
18-36786937-C-T			Likely benign (Dec 01, 2022)
18-36796898-T-G			Likely benign (Feb 01, 2023)
18-36796921-T-G		not specified	Uncertain significance (May 20, 2024)
18-36796972-G-C		not specified	Uncertain significance (Dec 03, 2021)
18-36797020-A-G		not specified	Uncertain significance (Mar 05, 2024)
18-36800212-T-C		not specified	Uncertain significance (Mar 16, 2024)
18-36800225-A-T		not specified	Uncertain significance (Sep 26, 2023)
18-36800242-T-C		not specified	Uncertain significance (Nov 08, 2021)
18-36800260-A-G		not specified	Uncertain significance (Dec 01, 2022)
18-36800283-G-C		not specified	Uncertain significance (May 17, 2023)
18-36800297-G-T		not specified	Uncertain significance (Feb 06, 2024)
18-36805452-T-A		not specified	Uncertain significance (Dec 26, 2023)
18-36818937-T-C		not specified	Uncertain significance (May 30, 2024)
18-36828745-G-A		not specified	Uncertain significance (Dec 21, 2021)
18-36829152-C-T		not specified	Uncertain significance (Jan 24, 2024)
18-36829157-C-T			Benign (Feb 02, 2018)
18-36829161-C-T		not specified	Uncertain significance (Sep 26, 2023)
18-36829179-C-A		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPGS2	protein_coding	protein_coding	ENST00000334295	7	49172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000147	0.876	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0265	165	164	1.01	0.00000788	1971
Missense in Polyphen		44	45.989	0.95675		612
Synonymous	0.817	55	63.3	0.869	0.00000319	579
Loss of Function	1.40	8	13.6	0.589	5.74e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000437	0.000437
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000166	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000801	0.0000791
Middle Eastern	0.000166	0.000163
South Asian	0.0000980	0.0000980
Other	0.000506	0.000489

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0784

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0709
• hipred: N
• hipred_score: 0.204
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Tpgs2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; skeleton phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein polyglutamylation
• Cellular component: cytoplasm;microtubule