CTSH

cathepsin H, the group of Cathepsins|Minor histocompatibility antigens

Basic information

Region (hg38): 15:78921058-78949574

Previous symbols: [ "CPSB" ]

Links

ENSG00000103811 ∙ NCBI:1512 ∙ OMIM:116820 ∙ HGNC:2535 ∙ Uniprot:P09668 ∙ 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 CTSH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSH 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				3	3	6
missense			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding				1		1
Total	0	0	16	6	4

Variants in CTSH

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

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

Position	Type	Phenotype	Significance	ClinVar
15-78922189-G-A		CTSH-related disorder	Likely benign (Nov 09, 2022)
15-78922192-C-T		not specified	Uncertain significance (May 23, 2024)
15-78922996-T-A		not specified	Uncertain significance (Sep 22, 2023)
15-78923025-T-G		not specified	Uncertain significance (Dec 07, 2021)
15-78923062-T-C		not specified	Uncertain significance (Mar 19, 2024)
15-78925349-G-C		not specified	Likely benign (May 14, 2024)
15-78925355-T-C		not specified	Uncertain significance (Dec 21, 2021)
15-78925362-T-C		not specified	Uncertain significance (Feb 28, 2024)
15-78927712-C-T			Likely benign (Jul 11, 2018)
15-78927771-C-A		not specified	Uncertain significance (Aug 21, 2023)
15-78929435-C-G		not specified	Uncertain significance (Apr 15, 2024)
15-78931491-C-T		not specified	Uncertain significance (Dec 23, 2022)
15-78931509-GGAA-G			Likely benign (Jul 31, 2018)
15-78932375-GGACA-G		Variant of unknown significance	Uncertain significance (Aug 08, 2013)
15-78932389-C-T		not specified	Uncertain significance (May 23, 2023)
15-78932401-C-T		not specified	Uncertain significance (Apr 18, 2023)
15-78935075-G-A		not specified	Uncertain significance (Jan 07, 2022)
15-78935684-G-A		not specified	Uncertain significance (Nov 29, 2021)
15-78935730-C-G		not specified	Uncertain significance (Oct 18, 2021)
15-78937337-A-G			Benign (Jun 12, 2018)
15-78937338-T-C		not specified	Uncertain significance (Jul 09, 2021)
15-78937341-T-C		not specified	Uncertain significance (Jan 08, 2024)
15-78937349-G-A		CTSH-related disorder	Likely benign (Feb 14, 2023)
15-78937358-C-T			Likely benign (Nov 08, 2018)
15-78937403-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSH	protein_coding	protein_coding	ENST00000220166	12	28517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.25e-8	0.804	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.535	170	191	0.891	0.0000104	2188
Missense in Polyphen		60	78.507	0.76426		893
Synonymous	-0.880	82	72.5	1.13	0.00000438	593
Loss of Function	1.52	16	24.0	0.666	0.00000119	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00122	0.00122
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00315	0.00316
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000309	0.000308
Middle Eastern	0.00315	0.00316
South Asian	0.000490	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for the overall degradation of proteins in lysosomes.
• Pathway: Lysosome - Homo sapiens (human);Apoptosis - Homo sapiens (human);Neutrophil degranulation;Surfactant metabolism;Metabolism of proteins;MHC class II antigen presentation;Innate Immune System;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.324

Intolerance Scores

• loftool: 0.448
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.197
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctsh
• Phenotype: respiratory system phenotype; normal phenotype; vision/eye phenotype

Gene ontology

• Biological process: metanephros development;T cell mediated cytotoxicity;adaptive immune response;immune response-regulating signaling pathway;proteolysis;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of cell population proliferation;positive regulation of gene expression;positive regulation of epithelial cell migration;neuropeptide catabolic process;bradykinin catabolic process;positive regulation of peptidase activity;antigen processing and presentation;positive regulation of cell migration;zymogen activation;protein destabilization;response to retinoic acid;membrane protein proteolysis;negative regulation of apoptotic process;surfactant homeostasis;neutrophil degranulation;cellular protein metabolic process;positive regulation of angiogenesis;proteolysis involved in cellular protein catabolic process;dichotomous subdivision of terminal units involved in lung branching;ERK1 and ERK2 cascade;cellular response to thyroid hormone stimulus;positive regulation of apoptotic signaling pathway
• Cellular component: extracellular region;extracellular space;lysosome;cytosol;secretory granule lumen;cytoplasmic ribonucleoprotein granule;intracellular membrane-bounded organelle;extracellular exosome;alveolar lamellar body;multivesicular body lumen;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: endopeptidase activity;aminopeptidase activity;cysteine-type endopeptidase activity;serine-type endopeptidase activity;protein binding;peptidase activity;cysteine-type peptidase activity;cysteine-type endopeptidase activator activity involved in apoptotic process;HLA-A specific activating MHC class I receptor activity;thyroid hormone binding