CELA3A

chymotrypsin like elastase 3A, the group of Chymotrypsin like elastases

Basic information

Region (hg38): 1:22001657-22012542

Previous symbols: [ "ELA3A" ]

Links

ENSG00000142789 ∙ NCBI:10136 ∙ OMIM:618693 ∙ HGNC:15944 ∙ Uniprot:P09093 ∙ 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 CELA3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELA3A 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				1		1
missense			29	4		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	5	0

Variants in CELA3A

This is a list of pathogenic ClinVar variants found in the CELA3A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-22001684-C-T		not specified	Uncertain significance (May 23, 2023)
1-22003014-G-A		not specified	Uncertain significance (Oct 04, 2024)
1-22003041-C-T		not specified	Uncertain significance (Oct 06, 2022)
1-22005451-C-T		not specified	Uncertain significance (Sep 30, 2024)
1-22005507-G-A		not specified	Uncertain significance (May 29, 2024)
1-22005665-G-C		not specified	Likely benign (Dec 22, 2023)
1-22005666-G-T		not specified	Uncertain significance (Oct 03, 2022)
1-22005667-A-C		not specified	Uncertain significance (Sep 29, 2022)
1-22005725-G-C		not specified	Uncertain significance (Dec 03, 2021)
1-22005729-G-T		not specified	Uncertain significance (Aug 02, 2021)
1-22006888-G-A		not specified	Uncertain significance (Jan 02, 2024)
1-22006930-G-A		not specified	Uncertain significance (Nov 19, 2024)
1-22006935-G-T		not specified	Uncertain significance (May 02, 2024)
1-22006954-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-22006958-G-T		not specified	Uncertain significance (Nov 08, 2024)
1-22006964-T-A		not specified	Uncertain significance (Nov 21, 2024)
1-22006979-C-T		not specified	Uncertain significance (Jun 29, 2022)
1-22007391-A-C		not specified	Uncertain significance (Mar 29, 2022)
1-22007392-C-G		not specified	Uncertain significance (Oct 26, 2021)
1-22007409-G-A		not specified	Uncertain significance (Aug 07, 2023)
1-22007420-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-22007462-A-T		not specified	Likely benign (Dec 28, 2023)
1-22007501-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-22007505-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-22009738-G-A		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELA3A	protein_coding	protein_coding	ENST00000290122	8	10884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.05e-9	0.284	125467	2	212	125681	0.000852

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.790	196	167	1.17	0.0000100	1720
Missense in Polyphen		61	62.57	0.97491		672
Synonymous	-1.72	87	68.9	1.26	0.00000458	532
Loss of Function	0.637	14	16.8	0.832	9.15e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00509	0.00509
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000328	0.000327
Finnish	0.00	0.00
European (Non-Finnish)	0.000396	0.000396
Middle Eastern	0.000328	0.000327
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Efficient protease with alanine specificity but only little elastolytic activity.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.346
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.694
• hipred: N
• hipred_score: 0.112
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cela3b

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space
• Molecular function: serine-type endopeptidase activity