CELA2A

chymotrypsin like elastase 2A, the group of Chymotrypsin like elastases

Basic information

Region (hg38): 1:15456728-15472091

Links

ENSG00000142615 ∙ NCBI:63036 ∙ OMIM:609443 ∙ HGNC:24609 ∙ Uniprot:P08217 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• abdominal obesity-metabolic syndrome 4 (Limited), mode of inheritance: AD
• abdominal obesity-metabolic syndrome 4 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Abdominal obesity-metabolic syndrome 4	AD	Cardiovascular	Among other features, individuals have been described with relatively early-onset cardiac disease, including myocardial infarction, and awareness may allow early interventions to ameliorate cardiovascular and related sequelae	Cardiovascular; Endocrine	31358993

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CELA2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELA2A 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		1	13	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	13	2	0

Variants in CELA2A

This is a list of pathogenic ClinVar variants found in the CELA2A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-15457115-C-T		not specified	Uncertain significance (Jun 13, 2024)
1-15457149-C-T		not specified	Uncertain significance (May 18, 2023)
1-15461588-A-C		not specified	Likely benign (Sep 29, 2022)
1-15461640-C-T		Hypertensive disorder;Hypertriglyceridemia;Diabetes;Coronary artery disorder • Abdominal obesity-metabolic syndrome 4 • CELA2A-related disorder	Pathogenic (May 04, 2022)
1-15462740-A-G		not specified	Uncertain significance (Sep 17, 2021)
1-15462752-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-15462758-C-A		Coronary artery disorder;Diabetes;Hypertriglyceridemia;Hypertensive disorder • Abdominal obesity-metabolic syndrome 4	Pathogenic (Oct 10, 2019)
1-15462783-C-T		not specified	Uncertain significance (Mar 15, 2024)
1-15462809-G-T			Likely benign (Jul 01, 2024)
1-15462824-G-A		not specified	Uncertain significance (Nov 09, 2023)
1-15463390-G-A		Coronary artery disorder;Diabetes;Hypertriglyceridemia;Hypertensive disorder • Abdominal obesity-metabolic syndrome 4	Pathogenic (Oct 10, 2019)
1-15466001-A-T		not specified	Uncertain significance (Nov 17, 2022)
1-15466005-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-15466035-G-A		not specified	Uncertain significance (Mar 11, 2024)
1-15466073-G-A		not specified	Uncertain significance (Feb 08, 2023)
1-15466127-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-15466137-G-C		not specified	Uncertain significance (Mar 08, 2024)
1-15466143-A-G		not specified	Uncertain significance (Jan 23, 2024)
1-15466145-G-C		Coronary artery disorder;Diabetes;Hypertriglyceridemia;Hypertensive disorder • Abdominal obesity-metabolic syndrome 4	Pathogenic (Oct 11, 2019)
1-15467429-G-A		not specified	Likely benign (Dec 21, 2023)
1-15467443-G-A			Uncertain significance (Nov 22, 2022)
1-15467497-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-15467537-C-T		not specified	Uncertain significance (Jan 31, 2023)
1-15471994-T-C		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELA2A	protein_coding	protein_coding	ENST00000359621	8	15364

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-16	0.00105	125665	1	80	125746	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0359	172	173	0.992	0.0000111	1732
Missense in Polyphen		64	64.39	0.99394		697
Synonymous	-0.352	83	79.0	1.05	0.00000573	554
Loss of Function	-1.21	21	15.8	1.33	7.78e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00115
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000653	0.000653
South Asian	0.000752	0.000752
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts upon elastin.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Intolerance Scores

• loftool: 0.325
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cela2a

Gene ontology

• Biological process: proteolysis;cornification
• Cellular component: extracellular region;extracellular space;cytosol;keratohyalin granule
• Molecular function: endopeptidase activity;serine-type endopeptidase activity;serine hydrolase activity