CELA3A

protein-coding

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

Gene summary

Elastases form a subfamily of serine proteases that hydrolyze many proteins in addition to elastin. Humans have six elastase genes which encode the structurally similar proteins elastase 1, 2, 2A, 2B, 3A, and 3B. Unlike other elastases, elastase 3A has little elastolytic activity. Like most of the human elastases, elastase 3A is secreted from the pancreas as a zymogen and, like other serine proteases such as trypsin, chymotrypsin and kallikrein, it has a digestive function in the intestine. Elastase 3A preferentially cleaves proteins after alanine residues. Elastase 3A may also function in the intestinal transport and metabolism of cholesterol. Both elastase 3A and elastase 3B have been referred to as protease E and as elastase 1. [provided by RefSeq, Jul 2008]

Previous symbols:

ELA3A

MANE transcript

NM_005747.5

Inheritance

—

ClinVar variants

U:58B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr1:22,001,657-22,012,542

External References & Databases

Ensembl (ENSG00000142789)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CELA3A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005747.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			58 clinvar	6 clinvar		64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	8	0	66

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005747.5	RefSeq	NP_005738.4	8	MANE Select
ENST00000290122.8	Ensembl	ENSP00000290122.3	8	MANE Select
ENST00000400271.2	Ensembl	ENSP00000383130.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein digestion and absorption - Homo sapiens (human)
Pancreatic secretion - Homo sapiens (human)

Biological Process

proteolysis

Molecular Function

serine-type endopeptidase activity

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290122
Coding exons: 8
Length: 10884
Individuals with no LoFs: 125467
Homozygous LoFs: 2
Heterozygous LoFs: 212
Defined: 125681
p: 0.000852

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.790	196	167	1.17	0.0000100	1720
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.0043	0.0043	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00040	0.00040	rare
South Asian	0.000065	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Efficient protease with alanine specificity but only little elastolytic activity.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.346
RVIS EVS: -0.36
RVIS percentile EVS: 29.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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