SCRN2

secernin 2

Basic information

Region (hg38): 17:47837692-47841289

Links

ENSG00000141295 ∙ NCBI:90507 ∙ OMIM:614966 ∙ HGNC:30381 ∙ Uniprot:Q96FV2 ∙ 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 SCRN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCRN2 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			46	5		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	5	0

Variants in SCRN2

This is a list of pathogenic ClinVar variants found in the SCRN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47837864-C-G		not specified	Uncertain significance (Oct 01, 2024)
17-47837879-C-T		not specified	Uncertain significance (Dec 10, 2024)
17-47837890-C-T		not specified	Uncertain significance (Mar 03, 2022)
17-47837906-G-A		not specified	Uncertain significance (Jul 15, 2024)
17-47837918-A-C		not specified	Uncertain significance (Jan 18, 2025)
17-47837921-C-T		not specified	Uncertain significance (Oct 27, 2022)
17-47837923-C-A		not specified	Uncertain significance (Jan 10, 2025)
17-47837924-C-T		not specified	Likely benign (Apr 07, 2022)
17-47837942-T-C		not specified	Likely benign (Jan 10, 2023)
17-47837948-C-G		not specified	Uncertain significance (Jan 04, 2022)
17-47837987-G-C		not specified	Uncertain significance (Jan 31, 2024)
17-47838326-G-A		not specified	Uncertain significance (Jun 12, 2023)
17-47838328-C-T		not specified	Uncertain significance (Sep 10, 2024)
17-47838349-C-G		not specified	Uncertain significance (Dec 21, 2023)
17-47838349-C-T		not specified	Uncertain significance (Mar 17, 2023)
17-47838379-C-T		not specified	Uncertain significance (Jan 22, 2025)
17-47838546-G-A		not specified	Uncertain significance (Oct 04, 2024)
17-47838555-A-G		not specified	Uncertain significance (Mar 10, 2025)
17-47838568-A-G		not specified	Uncertain significance (Jan 17, 2025)
17-47838572-C-G		not specified	Uncertain significance (May 28, 2024)
17-47838583-C-A		not specified	Uncertain significance (Nov 29, 2023)
17-47838616-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-47838630-G-A		not specified	Uncertain significance (Aug 26, 2022)
17-47838639-C-T		not specified	Uncertain significance (Feb 06, 2024)
17-47838797-G-A		not specified	Likely benign (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCRN2	protein_coding	protein_coding	ENST00000290216	7	3642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.74e-12	0.0610	125598	0	150	125748	0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.217	251	261	0.962	0.0000163	2723
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00194	0.00193
Ashkenazi Jewish	0.000896	0.000893
East Asian	0.000231	0.000217
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000482	0.000466
Middle Eastern	0.000231	0.000217
South Asian	0.00111	0.00108
Other	0.000514	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.943
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.8

Haploinsufficiency Scores

• pHI: 0.0998
• hipred: N
• hipred_score: 0.197
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scrn2

Gene ontology

• Biological process: proteolysis;exocytosis;biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function;protein binding;dipeptidase activity