CTSV

cathepsin V, the group of Cathepsins

Basic information

Region (hg38): 9:97029677-97156556

Previous symbols: [ "CTSL2" ]

Links

ENSG00000136943 ∙ NCBI:1515 ∙ OMIM:603308 ∙ HGNC:2538 ∙ Uniprot:O60911 ∙ 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 CTSV gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSV 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	1

Variants in CTSV

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

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

Position	Type	Phenotype	Significance	ClinVar
9-97032996-T-C		not specified	Likely benign (Aug 16, 2022)
9-97035544-G-C		not specified	Uncertain significance (Jan 07, 2022)
9-97035594-C-A		not specified	Uncertain significance (Feb 17, 2024)
9-97035594-C-T		not specified	Uncertain significance (Jan 10, 2023)
9-97035596-A-G		not specified	Uncertain significance (Apr 25, 2023)
9-97035627-G-T		not specified	Uncertain significance (Aug 30, 2021)
9-97035654-T-C		not specified	Uncertain significance (Apr 28, 2023)
9-97036543-A-C		not specified	Uncertain significance (Jan 27, 2022)
9-97036607-A-G			Benign (Jun 21, 2018)
9-97036617-T-C		not specified	Uncertain significance (Dec 05, 2022)
9-97036632-C-T		not specified	Likely benign (Feb 27, 2023)
9-97036653-T-C		not specified	Uncertain significance (Jul 25, 2023)
9-97036701-T-G		not specified	Uncertain significance (Apr 15, 2024)
9-97037322-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-97037329-G-T		not specified	Uncertain significance (Mar 25, 2024)
9-97037340-C-G		not specified	Uncertain significance (Jul 09, 2021)
9-97037347-T-C		not specified	Uncertain significance (Sep 14, 2023)
9-97037614-T-A		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSV	protein_coding	protein_coding	ENST00000259470	7	6986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.30e-7	0.483	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.289	177	188	0.941	0.0000103	2218
Missense in Polyphen		48	69.073	0.69492		867
Synonymous	0.0908	71	72.0	0.986	0.00000450	602
Loss of Function	0.833	12	15.5	0.772	7.24e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000782	0.000770
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000164	0.000163
Finnish	0.0000970	0.0000924
European (Non-Finnish)	0.000278	0.000273
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.000342	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cysteine protease. May have an important role in corneal physiology. {ECO:0000269|PubMed:10029531, ECO:0000269|PubMed:9727401}.
• Pathway: Lysosome - Homo sapiens (human);Apoptosis - Homo sapiens (human);Endochondral Ossification;Assembly of collagen fibrils and other multimeric structures;Gene expression (Transcription);Generic Transcription Pathway;Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;RNA Polymerase II Transcription;Collagen formation;Extracellular matrix organization;MHC class II antigen presentation;Innate Immune System;Immune System;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix;RUNX1 regulates transcription of genes involved in differentiation of keratinocytes;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.604
• hipred: N
• hipred_score: 0.112
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctsl
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: spermatogenesis;cellular response to starvation;response to glucose;multicellular organism aging;antigen processing and presentation of exogenous peptide antigen via MHC class II;nerve development;extracellular matrix disassembly;response to gonadotropin;regulation of keratinocyte differentiation;decidualization;autophagic cell death;response to glucocorticoid;proteolysis involved in cellular protein catabolic process;Sertoli cell differentiation;response to odorant
• Cellular component: extracellular region;extracellular space;lysosome;microvillus;external side of plasma membrane;secretory granule;neuron projection;lysosomal lumen;perikaryon;apical part of cell
• Molecular function: aminopeptidase activity;cysteine-type endopeptidase activity;serine-type endopeptidase activity;protein binding;cysteine-type peptidase activity;kininogen binding;peptide binding;protein-containing complex binding