CTRL

protein-coding

chymotrypsin like

Gene summary

This gene encodes a serine-type endopeptidase with chymotrypsin- and elastase-2-like activities. The gene encoding this zymogen is expressed specifically in the pancreas and likely functions as a digestive enzyme. [provided by RefSeq, Sep 2016]

MANE transcript

NM_001907.3

Inheritance

—

ClinVar variants

U:48B:9

Top phenotype

Long QT syndrome

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr16:67,927,640-67,932,365

External References & Databases

Ensembl (ENSG00000141086)

Transcript & Mutation Effects

hg38 • Region Span ~4.7 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 CTRL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 7

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001907.3. 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			46 clinvar	4 clinvar	3 clinvar	53
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	48	5	4	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001907.3	RefSeq	NP_001898.1	7	MANE Select
ENST00000574481.6	Ensembl	ENSP00000458537.2	7	MANE Select
ENST00000571044.5	Ensembl	ENSP00000461842.1	6	Standard
ENST00000571605.1	Ensembl	ENSP00000458598.1	6	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
protein catabolic process

Molecular Function

serine-type endopeptidase activity
serine-type peptidase activity

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000574481
Coding exons: 7
Length: 4775
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125745
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0908	165	162	1.02	0.00000992	1677
Missense (PolyPhen)		61	60.385	1.0102		690
Synonymous	-0.693	77	69.6	1.11	0.00000493	558
Loss of Function	0.0916	14	14.4	0.974	7.11e-7	138

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0990

Intolerance Scores

LoFtool: 0.245
RVIS EVS: 0.6
RVIS percentile EVS: 82.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0392

Gene Damage Prediction

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