SCRN3

secernin 3

Basic information

Region (hg38): 2:174395729-174429575

Links

ENSG00000144306 ∙ NCBI:79634 ∙ OMIM:614967 ∙ HGNC:30382 ∙ Uniprot:Q0VDG4 ∙ 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 SCRN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCRN3 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			23			23
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	1

Variants in SCRN3

This is a list of pathogenic ClinVar variants found in the SCRN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-174398311-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-174398366-A-G		not specified	Uncertain significance (Apr 05, 2023)
2-174398441-A-C		not specified	Uncertain significance (Jan 17, 2024)
2-174399926-C-A		not specified	Uncertain significance (Aug 09, 2021)
2-174399929-A-G		not specified	Uncertain significance (Feb 07, 2023)
2-174399952-G-C		not specified	Uncertain significance (Apr 22, 2022)
2-174399964-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-174401061-G-A		not specified	Uncertain significance (Apr 27, 2023)
2-174401143-G-C		not specified	Uncertain significance (Jun 11, 2021)
2-174401150-G-A		not specified	Uncertain significance (Apr 20, 2024)
2-174404111-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-174404135-A-G		not specified	Uncertain significance (Jun 27, 2022)
2-174404146-G-C		not specified	Uncertain significance (Oct 30, 2023)
2-174404153-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-174404174-A-C		not specified	Uncertain significance (Apr 25, 2022)
2-174404244-T-C		not specified	Uncertain significance (Jul 06, 2021)
2-174404253-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-174404306-A-C		not specified	Uncertain significance (Dec 12, 2023)
2-174422891-T-C		not specified	Uncertain significance (Apr 28, 2022)
2-174422917-C-A		not specified	Uncertain significance (Apr 08, 2024)
2-174422974-A-G		not specified	Uncertain significance (Nov 29, 2023)
2-174422990-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-174424540-C-T		not specified	Uncertain significance (May 30, 2024)
2-174424584-C-A		not specified	Uncertain significance (Jan 03, 2024)
2-174424603-T-C		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCRN3	protein_coding	protein_coding	ENST00000272732	7	33846

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-7	0.627	125562	2	182	125746	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0230	219	218	1.00	0.0000104	2799
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000745	0.000740
Ashkenazi Jewish	0.00	0.00
East Asian	0.000889	0.000870
Finnish	0.000470	0.000462
European (Non-Finnish)	0.00123	0.00113
Middle Eastern	0.000889	0.000870
South Asian	0.000206	0.000196
Other	0.000865	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0976

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.167
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.184

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scrn3

Gene ontology

• Biological process: proteolysis;exocytosis
• Molecular function: dipeptidase activity