SCRN1

protein-coding

secernin 1

Gene summary

This gene likely encodes a member of the secernin family of proteins. A similar protein in rat functions in regulation of exocytosis in mast cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

MANE transcript

NM_014766.5

Inheritance

—

ClinVar variants

U:58B:3

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr7:29,920,104-29,990,289

External References & Databases

Ensembl (ENSG00000136193)

Transcript & Mutation Effects

hg38 • Region Span ~70.2 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 SCRN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

Prostate cancerTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014766.5. 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			1 clinvar			1
missense			55 clinvar	3 clinvar		58
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	58	3	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014766.5	RefSeq	NP_055581.3	7	MANE Select
ENST00000242059.10	Ensembl	ENSP00000242059.5	7	MANE Select
NM_001145513.1	RefSeq	NP_001138985.1	7	Standard
NM_001145514.1	RefSeq	NP_001138986.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
exocytosis

Molecular Function

molecular_function
protein binding
dipeptidase activity

Cellular Component

nucleus
cytoplasm
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000434476
Coding exons: 8
Length: 70187
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.906	216	257	0.841	0.0000146	2872
Missense (PolyPhen)		57	87.086	0.65453		963
Synonymous	-0.515	106	99.5	1.07	0.00000658	812
Loss of Function	2.60	8	20.8	0.384	8.85e-7	245

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates exocytosis in mast cells. Increases both the extent of secretion and the sensitivity of mast cells to stimulation with calcium (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0785

Intolerance Scores

LoFtool: 0.664
RVIS EVS: 0.2
RVIS percentile EVS: 67.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.534

Gene Damage Prediction

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