CMA1

chymase 1, the group of Granule associated serine proteases of immune defence

Basic information

Region (hg38): 14:24505352-24508265

Links

ENSG00000092009 ∙ NCBI:1215 ∙ OMIM:118938 ∙ HGNC:2097 ∙ Uniprot:P23946 ∙ 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 CMA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMA1 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	15	1	0

Variants in CMA1

This is a list of pathogenic ClinVar variants found in the CMA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24505556-T-G		not specified	Uncertain significance (Mar 19, 2024)
14-24505611-C-T		not specified	Uncertain significance (Jan 26, 2022)
14-24505634-C-G		not specified	Uncertain significance (May 31, 2023)
14-24506060-C-T		not specified	Uncertain significance (May 05, 2023)
14-24506065-C-A		not specified	Uncertain significance (Dec 28, 2023)
14-24506081-G-A		not specified	Uncertain significance (Jul 06, 2021)
14-24506119-A-G		not specified	Uncertain significance (Nov 09, 2022)
14-24506140-T-C		not specified	Uncertain significance (Dec 07, 2021)
14-24506158-G-A		not specified	Uncertain significance (Oct 06, 2023)
14-24506160-C-A		not specified	Uncertain significance (Jun 17, 2024)
14-24506194-C-T		not specified	Uncertain significance (Sep 14, 2022)
14-24506558-C-A		not specified	Uncertain significance (Feb 28, 2024)
14-24506604-C-T		not specified	Likely benign (Nov 03, 2023)
14-24507388-G-T		not specified	Uncertain significance (Oct 03, 2022)
14-24507392-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
14-24507420-T-C		not specified	Uncertain significance (Dec 03, 2021)
14-24507429-C-G			Likely benign (Mar 28, 2018)
14-24507430-G-T		not specified	Uncertain significance (Dec 26, 2023)
14-24507488-G-C		not specified	Uncertain significance (Jul 06, 2021)
14-24507495-C-T		not specified	Uncertain significance (Jun 27, 2022)
14-24508192-G-C		not specified	Uncertain significance (May 20, 2024)
14-24508196-A-G		not specified	Uncertain significance (Apr 08, 2024)
14-24508216-G-C		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMA1	protein_coding	protein_coding	ENST00000250378	5	2913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.59e-9	0.0431	125014	4	714	125732	0.00286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.75	201	142	1.41	0.00000782	1589
Missense in Polyphen		76	51.795	1.4673		604
Synonymous	-1.90	74	55.9	1.32	0.00000300	519
Loss of Function	-0.806	11	8.47	1.30	3.56e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00602	0.00604
Ashkenazi Jewish	0.00	0.00
East Asian	0.0314	0.0314
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000795	0.0000791
Middle Eastern	0.0314	0.0314
South Asian	0.000392	0.000392
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major secreted protease of mast cells with suspected roles in vasoactive peptide generation, extracellular matrix degradation, and regulation of gland secretion.
• Pathway: Agents Acting on the Renin-Angiotensin System Pathway, Pharmacodynamics;Renin-angiotensin system - Homo sapiens (human);ACE Inhibitor Pathway, Pharmacodynamics;Lung fibrosis;ACE Inhibitor Pathway;Signal Transduction;Peptide hormone metabolism;Metabolism of proteins;Metabolism of Angiotensinogen to Angiotensins;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix;Signaling by SCF-KIT;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.626

Intolerance Scores

• loftool: 0.477
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.216
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cma1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: angiotensin maturation;extracellular matrix disassembly;midbrain development;basement membrane disassembly;positive regulation of angiogenesis;interleukin-1 beta biosynthetic process;regulation of inflammatory response;cellular response to glucose stimulus
• Cellular component: extracellular region;extracellular space;cytoplasm;secretory granule;collagen-containing extracellular matrix
• Molecular function: endopeptidase activity;serine-type endopeptidase activity;serine-type peptidase activity;peptide binding