CAT

catalase

Basic information

Region (hg38): 11:34438933-34472060

Links

ENSG00000121691 ∙ NCBI:847 ∙ OMIM:115500 ∙ HGNC:1516 ∙ Uniprot:P04040 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• acatalasia (Supportive), mode of inheritance: AR
• acatalasia (Strong), mode of inheritance: AR
• acatalasia (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Acatalasemia	AR	Allergy/Immunology/Infectious; Pharmacogenomic	Individuals may be prone to manifestations such as oral ulcers and gangrene, and prompt treatment of infections may be beneficial; Pharmacogenomically, variants may be related to adverse reactions with treatment with medications such as uric acid oxidase	Allergy/Immunology/Infectious	12991731; 13904105; 2308162; 1999334; 1591863; 1551654; 8673475; 11117918; 11001624; 11197178; 11603354; 11500062; 15771551; 15800961; 17729111

ClinVar

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

• not provided (21 variants)
• Inborn genetic diseases (9 variants)
• Acatalasia (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAT 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				5	5	10
missense			8	5	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region				1	2	3
non coding						0
Total	0	2	8	10	7

Highest pathogenic variant AF is 0.0000197

Variants in CAT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-34438994-T-C			Benign (Oct 19, 2015)
11-34449321-C-CGA		Acatalasia	Pathogenic (Apr 01, 2000)
11-34450983-G-A			Benign (Aug 10, 2018)
11-34451031-C-T			Likely benign (May 15, 2018)
11-34451076-C-T			Benign (Dec 31, 2019)
11-34451102-A-T			Benign (Dec 31, 2019)
11-34452084-AT-A		Acatalasemia, japanese type	Pathogenic (Jan 01, 1995)
11-34452212-G-A		Acatalasemia, japanese type	Pathogenic (Mar 01, 1992)
11-34453135-C-A			Likely benign (Apr 24, 2018)
11-34453139-A-C		not specified	Uncertain significance (May 31, 2022)
11-34453164-C-T			Benign (Jul 23, 2018)
11-34453174-C-T			Benign (Dec 31, 2019)
11-34453839-A-T			Likely benign (Apr 12, 2018)
11-34453840-C-T		not specified	Likely benign (Nov 07, 2023)
11-34453862-G-T		not specified	Uncertain significance (Feb 01, 2023)
11-34456025-C-A		CAT-related disorder	Benign/Likely benign (Dec 31, 2019)
11-34456170-A-G			Likely benign (Dec 31, 2019)
11-34456194-C-T		not specified	Uncertain significance (May 24, 2023)
11-34456207-G-T		Acatalasia • CAT-related disorder	Conflicting classifications of pathogenicity (Jun 08, 2022)
11-34456758-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-34456813-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-34456818-G-C		Acatalasia	Likely pathogenic (Jan 25, 2023)
11-34461246-T-C			Likely benign (Dec 17, 2018)
11-34461249-A-G			Likely pathogenic (Aug 21, 2017)
11-34461361-C-T			Benign (Oct 19, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAT	protein_coding	protein_coding	ENST00000241052	13	33138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-10	0.597	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0780	316	312	1.01	0.0000188	3515
Missense in Polyphen		151	154.42	0.97784		1785
Synonymous	-0.346	112	107	1.04	0.00000624	982
Loss of Function	1.34	19	26.4	0.719	0.00000130	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00118
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000141
Middle Eastern	0.000326	0.000326
South Asian	0.000882	0.000850
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells including T-cells, B-cells, myeloid leukemia cells, melanoma cells, mastocytoma cells and normal and transformed fibroblast cells. {ECO:0000269|PubMed:7882369}.
• Disease: DISEASE: Acatalasemia (ACATLAS) [MIM:614097]: A metabolic disorder characterized by a total or near total loss of catalase activity in red cells. It is often associated with ulcerating oral lesions. Acatalasemia is inherited as an autosomal recessive trait. {ECO:0000269|PubMed:2308162}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Longevity regulating pathway - multiple species - Homo sapiens (human);Peroxisome - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Oxidative Stress Pathway (Erythrocyte);Pathway_PA165980337;Oxidative Stress Pathway (Erythrocyte);Oxidative Stress Regulatory Pathway (Erythrocyte);Disulfiram Action Pathway;Degradation of Superoxides;Ethanol Degradation;Tryptophan Metabolism;Selenium Micronutrient Network;Folate Metabolism;Amyotrophic lateral sclerosis (ALS);Oxidative Stress;Tryptophan metabolism;DNA Damage Response (only ATM dependent);Neutrophil degranulation;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Metabolism of proteins;Innate Immune System;Immune System;ethanol degradation IV;Peroxisomal protein import;Cellular responses to external stimuli;the igf-1 receptor and longevity;Tryptophan degradation;reactive oxygen species degradation;FoxO family signaling (Consensus)

Recessive Scores

• pRec: 0.950

Intolerance Scores

• loftool: 0.221
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.496
• hipred: Y
• hipred_score: 0.516
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cat
• Phenotype: neoplasm; 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to reactive oxygen species;osteoblast differentiation;ureteric bud development;response to hypoxia;protein targeting to peroxisome;triglyceride metabolic process;aging;cholesterol metabolic process;aerobic respiration;response to light intensity;UV protection;response to ozone;response to lead ion;positive regulation of phosphatidylinositol 3-kinase signaling;response to activity;response to inactivity;hemoglobin metabolic process;negative regulation of NF-kappaB transcription factor activity;response to estradiol;response to insulin;response to vitamin A;response to vitamin E;response to L-ascorbic acid;cellular response to oxidative stress;response to hydrogen peroxide;hydrogen peroxide catabolic process;negative regulation of apoptotic process;neutrophil degranulation;response to ethanol;response to cadmium ion;positive regulation of NF-kappaB transcription factor activity;protein tetramerization;protein homotetramerization;positive regulation of cell division;response to hyperoxia;response to fatty acid;cellular response to growth factor stimulus;response to phenylpropanoid;cellular oxidant detoxification
• Cellular component: extracellular region;mitochondrial intermembrane space;lysosome;peroxisome;peroxisomal membrane;peroxisomal matrix;endoplasmic reticulum;Golgi apparatus;cytosol;plasma membrane;focal adhesion;membrane;secretory granule lumen;intracellular membrane-bounded organelle;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: aminoacylase activity;catalase activity;signaling receptor binding;antioxidant activity;oxidoreductase activity, acting on peroxide as acceptor;enzyme binding;heme binding;identical protein binding;protein homodimerization activity;metal ion binding;NADP binding