CELA1

protein-coding

chymotrypsin like elastase 1, 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, pancreatic elastase 1 is not expressed in the pancreas. To date, elastase 1 expression has only been detected in skin keratinocytes. Clinical literature that describes human elastase 1 activity in the pancreas or fecal material is actually referring to chymotrypsin-like elastase family, member 3B. [provided by RefSeq, May 2009]

Previous symbols:

ELA1

MANE transcript

NM_001971.6

Inheritance

—

ClinVar variants

U:36B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr12:51,328,442-51,346,679

External References & Databases

Ensembl (ENSG00000139610)

Transcript & Mutation Effects

hg38 • Region Span ~18.2 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 CELA1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001971.6. 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			1 clinvar	1 clinvar		2
missense			34 clinvar	3 clinvar		37
nonsense						0
start loss						0
frameshift					2 clinvar	2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	36	4	2	42

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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_001971.6	RefSeq	NP_001962.3	8	MANE Select
ENST00000293636.2	Ensembl	ENSP00000293636.1	8	MANE Select
ENST00001126549.1	Ensembl	ENSP00000796354.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
proteolysis
inflammatory response
post-embryonic development
Wnt signaling pathway

Molecular Function

serine-type endopeptidase activity
metal ion binding

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293636
Coding exons: 8
Length: 18237
Individuals with no LoFs: 77253
Homozygous LoFs: 7435
Heterozygous LoFs: 41058
Defined: 125746
p: 0.216

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.704	127	151	0.839	0.00000857	1649
Missense (PolyPhen)		49	56.082	0.87373		613
Synonymous	-0.202	64	62.0	1.03	0.00000366	518
Loss of Function	1.62	8	14.7	0.543	6.27e-7	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.12	0.12	notable
Latino/Admixed American	0.15	0.14	notable
Ashkenazi Jewish	0.27	0.26	notable
East Asian	0.038	0.037	notable
Finnish	0.22	0.22	notable
European (Non-Finnish)	0.30	0.30	notable
South Asian	0.17	0.17	notable
Other	0.26	0.25	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts upon elastin.;

Recessive Scores

pRec: 0.564

Intolerance Scores

LoFtool: 0.291
RVIS EVS: 0.49
RVIS percentile EVS: 79.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0544

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High