TYSND1

trypsin like peroxisomal matrix peptidase 1

Basic information

Region (hg38): 10:70137981-70146700

Links

ENSG00000156521 ∙ NCBI:219743 ∙ OMIM:611017 ∙ HGNC:28531 ∙ Uniprot:Q2T9J0 ∙ 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 TYSND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TYSND1 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			41	1	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	1

Variants in TYSND1

This is a list of pathogenic ClinVar variants found in the TYSND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-70139940-G-A		not specified	Uncertain significance (Mar 28, 2024)
10-70139943-G-A		not specified	Uncertain significance (May 30, 2023)
10-70139958-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-70139959-G-A		not specified	Uncertain significance (Jun 29, 2022)
10-70139987-C-G		not specified	Uncertain significance (May 17, 2023)
10-70140009-C-T		not specified	Uncertain significance (Jun 24, 2022)
10-70140013-G-A		not specified	Uncertain significance (Feb 11, 2022)
10-70140066-G-A		not specified	Uncertain significance (Mar 29, 2022)
10-70140114-T-C		not specified	Uncertain significance (Mar 29, 2022)
10-70140120-C-T		not specified	Uncertain significance (Sep 26, 2023)
10-70140123-G-C		not specified	Uncertain significance (Sep 25, 2023)
10-70142685-T-G		not specified	Uncertain significance (Jan 04, 2024)
10-70142718-C-G		not specified	Uncertain significance (Feb 23, 2023)
10-70142722-G-A		not specified	Uncertain significance (Jan 16, 2024)
10-70142733-G-A		not specified	Uncertain significance (May 13, 2024)
10-70142749-C-T		not specified	Uncertain significance (Dec 16, 2023)
10-70142754-G-A		not specified	Likely benign (Dec 04, 2023)
10-70142807-G-C		not specified	Uncertain significance (Jan 05, 2022)
10-70142835-A-G		not specified	Uncertain significance (May 24, 2023)
10-70143868-G-A		not specified	Uncertain significance (Oct 20, 2021)
10-70143919-T-C		not specified	Uncertain significance (Jan 29, 2024)
10-70143925-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-70143955-C-G		not specified	Uncertain significance (Dec 03, 2021)
10-70145515-A-G		not specified	Uncertain significance (Jun 11, 2024)
10-70145590-C-A		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TYSND1	protein_coding	protein_coding	ENST00000287078	4	8696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000682	0.923	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.975	238	284	0.837	0.0000154	3466
Missense in Polyphen		80	90.999	0.87913		1135
Synonymous	2.75	91	131	0.695	0.00000738	1278
Loss of Function	1.57	7	13.1	0.533	5.70e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000119	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000547	0.0000527
Middle Eastern	0.000119	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Peroxisomal protease that mediates both the removal of the leader peptide from proteins containing a PTS2 target sequence and processes several PTS1-containing proteins. Catalyzes the processing of PTS1-proteins involved in the peroxisomal beta- oxidation of fatty acids. {ECO:0000269|PubMed:22002062}.
• Pathway: Metabolism of proteins;Peroxisomal protein import;TYSND1 cleaves peroxisomal proteins (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.312
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tysnd1
• Phenotype: liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: proteolysis;protein targeting to peroxisome;protein processing;regulation of fatty acid beta-oxidation;protein homooligomerization
• Cellular component: peroxisome;peroxisomal matrix;cytosol;membrane
• Molecular function: protease binding;serine-type endopeptidase activity