CTSW

cathepsin W, the group of Cathepsins

Basic information

Region (hg38): 11:65879809-65883741

Links

ENSG00000172543 ∙ NCBI:1521 ∙ OMIM:602364 ∙ HGNC:2546 ∙ Uniprot:P56202 ∙ 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 CTSW gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSW 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						0
missense			29	2		31
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in CTSW

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

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

Position	Type	Phenotype	Significance	ClinVar
11-65879876-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-65879879-TGCCTCCTG-T			Likely benign (Nov 01, 2022)
11-65880235-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-65880236-C-A		not specified	Uncertain significance (Dec 20, 2023)
11-65881424-G-C		not specified	Uncertain significance (Sep 29, 2023)
11-65881427-A-T		not specified	Uncertain significance (Aug 13, 2021)
11-65881428-T-A		not specified	Uncertain significance (Apr 28, 2022)
11-65881445-G-A		not specified	Uncertain significance (Oct 03, 2023)
11-65882208-G-A		not specified	Uncertain significance (Apr 04, 2024)
11-65882214-C-G		not specified	Uncertain significance (Dec 01, 2022)
11-65882222-G-A		not specified	Uncertain significance (Aug 15, 2023)
11-65882229-G-A		not specified	Uncertain significance (Apr 07, 2022)
11-65882306-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-65882309-A-G		not specified	Uncertain significance (Aug 02, 2022)
11-65882473-T-G		not specified	Uncertain significance (Nov 08, 2022)
11-65882482-T-C		not specified	Uncertain significance (Apr 25, 2022)
11-65882487-C-T		not specified	Uncertain significance (May 16, 2024)
11-65882509-T-C		not specified	Uncertain significance (Sep 25, 2023)
11-65882514-G-A		not specified	Uncertain significance (Sep 06, 2022)
11-65882520-G-A		not specified	Uncertain significance (Jun 28, 2022)
11-65882520-G-T		not specified	Uncertain significance (Jun 11, 2024)
11-65882619-C-A		not specified	Uncertain significance (Mar 07, 2023)
11-65882627-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-65882687-A-G		not specified	Uncertain significance (Jan 03, 2024)
11-65882890-A-C		not specified	Likely benign (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSW	protein_coding	protein_coding	ENST00000307886	10	3933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.86e-12	0.0676	125007	8	733	125748	0.00295

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.674	247	219	1.13	0.0000127	2456
Missense in Polyphen		85	82.144	1.0348		928
Synonymous	0.0453	87	87.5	0.994	0.00000530	737
Loss of Function	0.293	18	19.4	0.928	8.31e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0206	0.0206
Ashkenazi Jewish	0.000795	0.000794
East Asian	0.000500	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000500	0.000489
South Asian	0.000540	0.000523
Other	0.00326	0.00326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a specific function in the mechanism or regulation of T-cell cytolytic activity.
• Pathway: Lysosome - Homo sapiens (human);Apoptosis - Homo sapiens (human);Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.0985
• hipred: N
• hipred_score: 0.146
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctsw
• Phenotype: normal phenotype

Gene ontology

• Biological process: platelet degranulation;immune response;proteolysis involved in cellular protein catabolic process
• Cellular component: extracellular region;extracellular space;lysosome;membrane;platelet dense granule lumen
• Molecular function: cysteine-type endopeptidase activity;cysteine-type peptidase activity