TPSG1

tryptase gamma 1, the group of Serine proteases

Basic information

Region (hg38): 16:1221651-1225793

Links

ENSG00000116176 ∙ NCBI:25823 ∙ OMIM:609341 ∙ HGNC:14134 ∙ Uniprot:Q9NRR2 ∙ 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 TPSG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPSG1 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			37	6	1	44
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	37	7	2

Variants in TPSG1

This is a list of pathogenic ClinVar variants found in the TPSG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1221793-CAG-C			Likely benign (Apr 30, 2018)
16-1221819-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-1221820-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-1221877-G-A		not specified	Uncertain significance (Jul 19, 2022)
16-1221887-G-C		not specified	Uncertain significance (Jan 03, 2024)
16-1221898-C-T		not specified	Uncertain significance (May 18, 2023)
16-1221910-G-T			Likely benign (Feb 25, 2018)
16-1221925-A-T		not specified	Uncertain significance (Dec 06, 2022)
16-1221943-C-A		not specified	Uncertain significance (Aug 26, 2022)
16-1221946-T-G		not specified	Likely benign (May 23, 2024)
16-1221954-C-T		not specified	Uncertain significance (Jan 22, 2024)
16-1221958-G-A		not specified	Uncertain significance (Nov 10, 2021)
16-1221964-A-G		not specified	Uncertain significance (Oct 27, 2021)
16-1221970-C-T			Benign (Dec 13, 2017)
16-1221987-G-A		not specified	Uncertain significance (Aug 04, 2021)
16-1221999-G-A		not specified	Uncertain significance (Feb 03, 2022)
16-1222002-C-T		not specified	Uncertain significance (Oct 05, 2023)
16-1222012-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-1222057-C-T		not specified	Likely benign (Sep 20, 2023)
16-1222087-C-T		not specified	Uncertain significance (Apr 07, 2023)
16-1222210-C-T		not specified	Uncertain significance (Mar 31, 2024)
16-1222218-C-T		not specified	Likely benign (Oct 18, 2021)
16-1222276-G-A		not specified	Uncertain significance (Dec 18, 2023)
16-1222278-C-A		not specified	Uncertain significance (Nov 29, 2023)
16-1222306-T-C		not specified	Likely benign (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPSG1	protein_coding	protein_coding	ENST00000234798	6	3607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.59e-15	0.000653	125562	0	82	125644	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.45	300	202	1.48	0.0000138	1962
Missense in Polyphen		100	64.063	1.561		671
Synonymous	-3.45	137	94.4	1.45	0.00000659	730
Loss of Function	-2.39	17	9.19	1.85	3.92e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00175	0.00172
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000218
Finnish	0.0000532	0.0000462
European (Non-Finnish)	0.000203	0.000185
Middle Eastern	0.000223	0.000218
South Asian	0.000465	0.000457
Other	0.000359	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.315

Intolerance Scores

• loftool: 0.128
• rvis_EVS: 1.2
• rvis_percentile_EVS: 93.01

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.146
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpsg1

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space;integral component of plasma membrane
• Molecular function: serine-type endopeptidase activity;serine-type peptidase activity