TPSD1

tryptase delta 1

Basic information

Region (hg38): 16:1256059-1259008

Links

ENSG00000095917 ∙ NCBI:23430 ∙ OMIM:609272 ∙ HGNC:14118 ∙ Uniprot:Q9BZJ3 ∙ 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 TPSD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPSD1 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			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	2

Variants in TPSD1

This is a list of pathogenic ClinVar variants found in the TPSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1256294-C-T		not specified	Uncertain significance (Mar 01, 2024)
16-1256309-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-1256332-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-1256537-A-G		not specified	Likely benign (Jul 14, 2021)
16-1256540-C-T		not specified	Uncertain significance (Jul 14, 2021)
16-1256551-G-T		not specified	Uncertain significance (Jun 01, 2023)
16-1256608-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-1256632-G-C		not specified	Uncertain significance (Aug 15, 2023)
16-1256639-C-T		not specified	Uncertain significance (Nov 27, 2023)
16-1256645-T-A		not specified	Uncertain significance (Jan 04, 2022)
16-1256668-G-A		not specified	Uncertain significance (Apr 20, 2024)
16-1256669-C-G		not specified	Uncertain significance (Jan 23, 2024)
16-1256669-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-1256672-C-T		not specified	Uncertain significance (May 28, 2024)
16-1256677-T-A		not specified	Uncertain significance (Apr 09, 2024)
16-1256824-G-C		Bladder exstrophy-epispadias-cloacal extrophy complex	Uncertain significance (-)
16-1256835-G-A		not specified	Uncertain significance (Mar 18, 2024)
16-1256840-C-A		not specified	Uncertain significance (Apr 13, 2023)
16-1256897-C-G		not specified	Uncertain significance (Jun 24, 2022)
16-1256913-A-G		not specified	Uncertain significance (Mar 07, 2023)
16-1256918-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-1256936-C-A		not specified	Uncertain significance (May 16, 2023)
16-1256960-A-G		not specified	Likely benign (Mar 20, 2024)
16-1256963-T-A		not specified	Uncertain significance (Apr 04, 2023)
16-1256985-C-A		not specified	Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPSD1	protein_coding	protein_coding	ENST00000211076	5	2473

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.04e-12	0.0106	74442	8009	43240	125691	0.230

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.62	208	152	1.37	0.00000971	1502
Missense in Polyphen		69	54.576	1.2643		598
Synonymous	-2.47	98	71.4	1.37	0.00000529	466
Loss of Function	-0.946	15	11.5	1.30	5.97e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.767	0.761
Ashkenazi Jewish	0.337	0.325
East Asian	0.164	0.164
Finnish	0.158	0.158
European (Non-Finnish)	0.203	0.200
Middle Eastern	0.164	0.164
South Asian	0.185	0.183
Other	0.258	0.251

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type. {ECO:0000250}.

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.208
• rvis_EVS: 1.71
• rvis_percentile_EVS: 96.46

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.112
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.203

Gene Damage Prediction

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

Gene ontology

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