SCRN2

protein-coding

secernin 2

Gene summary

Predicted to enable cysteine-type exopeptidase activity and dipeptidase activity. Predicted to be involved in proteolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_138355.4

Inheritance

—

ClinVar variants

U:87B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr17:47,837,692-47,841,289

External References & Databases

Ensembl (ENSG00000141295)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 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 SCRN2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 89

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138355.4. 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
missense			84 clinvar	7 clinvar		91
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	87	7	0	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138355.4	RefSeq	NP_612364.2	7	MANE Select
ENST00000290216.14	Ensembl	ENSP00000290216.9	7	MANE Select
NM_001145023.2	RefSeq	NP_001138495.1	6	Standard
ENST00000407215.7	Ensembl	ENSP00000383935.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
exocytosis
biological_process

Molecular Function

molecular_function
protein binding
dipeptidase activity

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290216
Coding exons: 7
Length: 3642
Individuals with no LoFs: 125598
Homozygous LoFs: 0
Heterozygous LoFs: 150
Defined: 125748
p: 0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.217	251	261	0.962	0.0000163	2723
Missense (PolyPhen)		94	102.22	0.91957		1080
Synonymous	-0.0595	112	111	1.01	0.00000693	894
Loss of Function	0.251	18	19.2	0.938	9.18e-7	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00070	0.00067	rare
Ashkenazi Jewish	0.00090	0.00089	rare
East Asian	0.00023	0.00022	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00048	0.00047	rare
South Asian	0.0011	0.0011	notable
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0972

Intolerance Scores

LoFtool: 0.943
RVIS EVS: 0.76
RVIS percentile EVS: 86.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.355

Gene Damage Prediction

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