SCRN1

secernin 1

Basic information

Region (hg38): 7:29920103-29990289

Links

ENSG00000136193 ∙ NCBI:9805 ∙ OMIM:614965 ∙ HGNC:22192 ∙ Uniprot:Q12765 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCRN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCRN1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	22	1	1

Variants in SCRN1

This is a list of pathogenic ClinVar variants found in the SCRN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-29923318-C-T			Benign (Jul 15, 2020)
7-29923979-G-A		Malignant tumor of prostate	Uncertain significance (-)
7-29923994-T-C		not specified	Uncertain significance (Oct 05, 2023)
7-29924020-G-C		not specified	Uncertain significance (Feb 09, 2023)
7-29926469-T-C		not specified	Likely benign (May 27, 2022)
7-29926613-T-C		not specified	Uncertain significance (May 27, 2022)
7-29936585-G-C		not specified	Uncertain significance (Sep 26, 2022)
7-29936598-G-T		not specified	Uncertain significance (Jun 01, 2023)
7-29936613-G-A		not specified	Uncertain significance (Sep 30, 2021)
7-29936679-T-G		not specified	Uncertain significance (Nov 10, 2022)
7-29936716-T-C		not specified	Uncertain significance (May 21, 2024)
7-29936719-T-C		not specified	Uncertain significance (Oct 04, 2023)
7-29940714-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-29940766-C-T		not specified	Uncertain significance (Aug 31, 2022)
7-29940770-C-G		not specified	Uncertain significance (Jul 20, 2021)
7-29940780-C-G		not specified	Uncertain significance (Jul 12, 2023)
7-29944008-T-C		not specified	Uncertain significance (Sep 17, 2021)
7-29944013-T-C		not specified	Uncertain significance (Sep 01, 2021)
7-29944036-C-T		not specified	Uncertain significance (Oct 25, 2022)
7-29944037-G-A		not specified	Uncertain significance (Dec 14, 2021)
7-29955249-C-A		not specified	Uncertain significance (Mar 16, 2022)
7-29955316-T-C		not specified	Uncertain significance (Dec 18, 2023)
7-29955342-C-T		Malignant tumor of prostate	Uncertain significance (-)
7-29955351-T-C		not specified	Uncertain significance (Dec 12, 2022)
7-29968937-G-A		not specified	Uncertain significance (Jul 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCRN1	protein_coding	protein_coding	ENST00000434476	8	70187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00249	0.995	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	216	257	0.841	0.0000146	2872
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.286
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.534

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scrn1

Gene ontology

• Biological process: proteolysis;exocytosis
• Cellular component: nucleus;cytoplasm;nuclear membrane
• Molecular function: molecular_function;protein binding;dipeptidase activity