SCRN3

protein-coding

secernin 3

Gene summary

Predicted to enable cysteine-type exopeptidase activity and dipeptidase activity. Predicted to be involved in detection of temperature stimulus involved in sensory perception of pain. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024583.5

Inheritance

—

ClinVar variants

U:56B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr2:174,395,730-174,429,575

External References & Databases

Ensembl (ENSG00000144306)

Transcript & Mutation Effects

hg38 • Region Span ~33.8 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 SCRN3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 54

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024583.5. 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						0
missense			54 clinvar	2 clinvar		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	56	2	0	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024583.5	RefSeq	NP_078859.2	7	MANE Select
ENST00000272732.11	Ensembl	ENSP00000272732.6	7	MANE Select
NM_001193528.2	RefSeq	NP_001180457.1	8	Standard
NM_001412202.1	RefSeq	NP_001399131.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
exocytosis

Molecular Function

dipeptidase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272732
Coding exons: 7
Length: 33846
Individuals with no LoFs: 125562
Homozygous LoFs: 2
Heterozygous LoFs: 182
Defined: 125746
p: 0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0230	219	218	1.00	0.0000104	2799
Missense (PolyPhen)		62	66.897	0.9268		846
Synonymous	1.20	59	71.9	0.820	0.00000326	773
Loss of Function	1.11	13	18.1	0.719	8.25e-7	242

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00049	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00089	0.00087	rare
Finnish	0.00047	0.00046	rare
European (Non-Finnish)	0.0012	0.0011	notable
South Asian	0.00021	0.00020	rare
Other	0.00086	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0976

Intolerance Scores

LoFtool: 0.965
RVIS EVS: 0
RVIS percentile EVS: 53.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.184

Gene Damage Prediction

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