CELA2A

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

Basic information

Region (hg38): 1:15456728-15472091

Links

ENSG00000142615NCBI:63036OMIM:609443HGNC:24609Uniprot:P08217AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Abdominal obesity-metabolic syndrome 4ADCardiovascularAmong 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 sequelaeCardiovascular; Endocrine31358993

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
clinvar
13
clinvar
2
clinvar
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)3265709
1-15457149-C-T not specified Uncertain significance (May 18, 2023)2515678
1-15461588-A-C not specified Likely benign (Sep 29, 2022)2207009
1-15461640-C-T Abdominal obesity-metabolic syndrome 4 • Hypertriglyceridemia;Hypertensive disorder;Coronary artery disorder;Diabetes • CELA2A-related disorder Pathogenic/Likely pathogenic (Feb 29, 2024)633595
1-15462740-A-G not specified Uncertain significance (Sep 17, 2021)2408708
1-15462752-G-A not specified Uncertain significance (Aug 02, 2021)2240495
1-15462758-C-A Hypertensive disorder;Coronary artery disorder;Diabetes;Hypertriglyceridemia • Abdominal obesity-metabolic syndrome 4 Pathogenic (Oct 10, 2019)633593
1-15462783-C-T not specified Uncertain significance (Mar 15, 2024)3265711
1-15462809-G-T Likely benign (Jul 01, 2024)3257603
1-15462824-G-A not specified Uncertain significance (Nov 09, 2023)3141908
1-15463390-G-A Hypertensive disorder;Coronary artery disorder;Diabetes;Hypertriglyceridemia • Abdominal obesity-metabolic syndrome 4 Pathogenic (Oct 10, 2019)633592
1-15466001-A-T not specified Uncertain significance (Nov 17, 2022)2326372
1-15466005-G-A not specified Uncertain significance (Feb 16, 2023)2486220
1-15466035-G-A not specified Uncertain significance (Mar 11, 2024)3141910
1-15466073-G-A not specified Uncertain significance (Feb 08, 2023)2456239
1-15466127-G-A not specified Uncertain significance (Mar 31, 2024)3265708
1-15466137-G-C not specified Uncertain significance (Mar 08, 2024)3141911
1-15466143-A-G not specified Uncertain significance (Jan 23, 2024)3141912
1-15466145-G-C Hypertensive disorder;Coronary artery disorder;Diabetes;Hypertriglyceridemia • Abdominal obesity-metabolic syndrome 4 Pathogenic (Oct 11, 2019)633594
1-15467429-G-A not specified Likely benign (Dec 21, 2023)3141913
1-15467443-G-A Uncertain significance (Nov 22, 2022)2576051
1-15467497-G-A not specified Uncertain significance (Dec 20, 2023)3141914
1-15467537-C-T not specified Uncertain significance (Jan 31, 2023)2463962
1-15471994-T-C not specified Uncertain significance (Apr 04, 2024)3265710

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CELA2Aprotein_codingprotein_codingENST00000359621 815364
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.97e-160.001051256651801257460.000322
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.03591721730.9920.00001111732
Missense in Polyphen6464.390.99394697
Synonymous-0.3528379.01.050.00000573554
Loss of Function-1.212115.81.337.78e-7150

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001210.00115
Ashkenazi Jewish0.000.00
East Asian0.0006530.000653
Finnish0.000.00
European (Non-Finnish)0.0001760.000176
Middle Eastern0.0006530.000653
South Asian0.0007520.000752
Other0.0001630.000163

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

pHI
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cela2a
Phenotype

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