TPSAB1

tryptase alpha/beta 1

Basic information

Region (hg38): 16:1239266-1242554

Previous symbols: [ "TPSB1", "TPS1", "TPS2" ]

Links

ENSG00000172236 ∙ NCBI:7177 ∙ OMIM:191080 ∙ HGNC:12019 ∙ Uniprot:Q15661 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Irritable bowel syndrome, cutaneous complaints, connective tissue abnormalities, and dysautonomia	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Allergy/Immunology/Infectious; Gastrointestinal; Musculoskeletal; Neurologic	27749843
Reported pathogenic variants have involved gene duplications or triplications

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TPSAB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPSAB1 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	5	7
missense			20	2	11	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					18	18
Total	0	0	20	4	34

Variants in TPSAB1

This is a list of pathogenic ClinVar variants found in the TPSAB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1240834-C-A			Benign (May 15, 2021)
16-1240943-T-A		not specified	Uncertain significance (Feb 16, 2023)
16-1240962-G-A			Likely benign (Jun 01, 2023)
16-1240976-C-A		not specified	Uncertain significance (Mar 25, 2022)
16-1240985-C-T		not specified	Likely benign (Mar 19, 2024)
16-1241074-T-C			Benign (May 15, 2021)
16-1241113-C-G			Benign (May 15, 2021)
16-1241126-C-T			Benign (May 30, 2021)
16-1241174-G-A			Benign (May 05, 2021)
16-1241185-G-T		not specified	Uncertain significance (May 31, 2023)
16-1241189-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-1241237-G-C		not specified	Uncertain significance (Nov 13, 2023)
16-1241244-C-T			Benign (May 05, 2021)
16-1241260-C-T		not specified	Uncertain significance (Nov 12, 2021)
16-1241287-C-A		not specified	Uncertain significance (May 26, 2024)
16-1241287-C-T		not specified	Uncertain significance (May 03, 2023)
16-1241307-A-G			Benign (May 05, 2021)
16-1241317-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-1241317-G-C			Benign (May 05, 2021)
16-1241321-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-1241336-G-A			Benign (May 16, 2021)
16-1241354-G-C			Benign (May 15, 2021)
16-1241444-G-T		not specified	Uncertain significance (Jun 13, 2024)
16-1241453-G-A			Benign (May 05, 2021)
16-1241472-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPSAB1	protein_coding	protein_coding	ENST00000338844	5	1859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-13	0.00179	125578	0	79	125657	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.13	247	142	1.74	0.00000920	1694
Missense in Polyphen		85	50.925	1.6691		701
Synonymous	-4.38	110	65.1	1.69	0.00000483	531
Loss of Function	-1.90	16	9.63	1.66	5.56e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000949	0.000944
Ashkenazi Jewish	0.00	0.00
East Asian	0.000387	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000172	0.000141
Middle Eastern	0.000387	0.000381
South Asian	0.000856	0.000850
Other	0.000357	0.000326

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. May play a role in innate immunity. Isoform 2 cleaves large substrates, such as fibronectin, more efficiently than isoform 1, but seems less efficient toward small substrates (PubMed:18854315). {ECO:0000250, ECO:0000250|UniProtKB:P21845, ECO:0000269|PubMed:18854315}.
• Pathway: Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.483

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpsb2
• Phenotype: cellular phenotype; hematopoietic system phenotype; immune system phenotype; skeleton phenotype

Gene ontology

• Biological process: proteolysis;defense response;extracellular matrix disassembly
• Cellular component: extracellular region;extracellular space;collagen-containing extracellular matrix
• Molecular function: serine-type endopeptidase activity;protein binding;serine-type peptidase activity