SYS1-DBNDD2

SYS1-DBNDD2 readthrough (NMD candidate)

Basic information

Region (hg38): 20:45363199-45410610

Links

ENSG00000254806 ∙ NCBI:767557 ∙ ∙ HGNC:33535 ∙ ∙ ∙ 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 SYS1-DBNDD2 gene.

• Inborn genetic diseases (42 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYS1-DBNDD2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			38	6		44
Total	0	0	38	6	0

Variants in SYS1-DBNDD2

This is a list of pathogenic ClinVar variants found in the SYS1-DBNDD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45363536-C-A		not specified	Uncertain significance (Jun 14, 2023)
20-45363536-C-T		not specified	Uncertain significance (May 22, 2023)
20-45363539-G-C		not specified	Uncertain significance (Jan 19, 2022)
20-45363542-A-T		not specified	Uncertain significance (Dec 14, 2023)
20-45363550-A-T		not specified	Uncertain significance (Oct 03, 2022)
20-45363553-T-C		not specified	Uncertain significance (Aug 30, 2022)
20-45363631-C-T			Likely benign (Apr 01, 2023)
20-45365649-C-T		not specified	Uncertain significance (Jul 06, 2021)
20-45366988-C-T		not specified	Uncertain significance (Sep 22, 2023)
20-45366989-G-A			Likely benign (Apr 01, 2023)
20-45367062-C-T		not specified	Uncertain significance (Mar 12, 2024)
20-45367066-C-T		not specified	Uncertain significance (Mar 31, 2023)
20-45367105-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-45373915-A-G		not specified	Uncertain significance (Nov 15, 2021)
20-45375074-C-T		not specified	Uncertain significance (Dec 28, 2022)
20-45375095-G-A		not specified	Likely benign (Jan 03, 2022)
20-45375110-G-A		not specified	Uncertain significance (Aug 17, 2021)
20-45375136-C-T		not specified	Uncertain significance (Mar 01, 2023)
20-45375157-C-T		not specified	Uncertain significance (Jan 18, 2023)
20-45375232-T-C		not specified	Uncertain significance (Mar 16, 2022)
20-45375254-T-C		not specified	Likely benign (Jan 23, 2023)
20-45375254-T-G		not specified	Uncertain significance (Oct 26, 2022)
20-45375265-C-A		not specified	Uncertain significance (Jul 14, 2023)
20-45375319-G-A		not specified	Uncertain significance (Oct 14, 2023)
20-45375370-G-A		not specified	Uncertain significance (Jun 21, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.404

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene ontology

• Biological process: Golgi to endosome transport;protein localization to Golgi apparatus;Golgi to plasma membrane protein transport
• Cellular component: trans-Golgi network;cytosol;integral component of Golgi membrane