SYCN

syncollin

Basic information

Region (hg38): 19:39202824-39204263

Previous symbols: [ "INSSA1" ]

Links

ENSG00000179751 ∙ NCBI:342898 ∙ OMIM:620140 ∙ HGNC:18442 ∙ Uniprot:Q0VAF6 ∙ 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 SYCN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCN 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in SYCN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-39203884-T-A		not specified	Uncertain significance (Apr 07, 2022)
19-39203896-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-39203911-C-G		not specified	Uncertain significance (May 21, 2024)
19-39203939-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-39203942-C-T		not specified	Uncertain significance (May 23, 2024)
19-39203949-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-39203960-T-C		not specified	Uncertain significance (Jun 10, 2024)
19-39203987-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-39204004-G-A		not specified	Uncertain significance (May 29, 2024)
19-39204004-G-C		not specified	Uncertain significance (May 29, 2024)
19-39204136-T-C		not specified	Uncertain significance (Dec 03, 2021)
19-39204166-T-C		not specified	Uncertain significance (Oct 26, 2022)
19-39204176-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-39204223-A-T		not specified	Uncertain significance (Mar 29, 2022)
19-39204226-G-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCN	protein_coding	protein_coding	ENST00000318438	2	1436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000445	0.245	124269	0	46	124315	0.000185

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.166	89	84.7	1.05	0.00000500	819
Missense in Polyphen		29	32.508	0.89209		310
Synonymous	0.410	43	46.6	0.924	0.00000307	303
Loss of Function	-0.426	6	4.97	1.21	2.13e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000488	0.000474
Ashkenazi Jewish	0.000704	0.000698
East Asian	0.000395	0.000390
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.000105	0.0000977
Middle Eastern	0.000395	0.000390
South Asian	0.000299	0.000294
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in exocytosis in pancreatic acinar cells regulating the fusion of zymogen granules with each other. May have a pore-forming activity on membranes and regulate exocytosis in other exocrine tissues (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.243
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.203

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sycn
• Phenotype: immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: exocytosis
• Cellular component: transport vesicle membrane;secretory granule membrane