SYS1

SYS1 golgi trafficking protein

Basic information

Region (hg38): 20:45361937-45376798

Previous symbols: [ "C20orf169" ]

Links

ENSG00000204070 ∙ NCBI:90196 ∙ OMIM:612979 ∙ HGNC:16162 ∙ Uniprot:Q8N2H4 ∙ 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 SYS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYS1 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				2		2
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in SYS1

This is a list of pathogenic ClinVar variants found in the SYS1 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)
20-45363611-A-G		not specified	Uncertain significance (May 28, 2024)
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)
20-45367086-C-G		not specified	Uncertain significance (Aug 20, 2024)
20-45367105-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-45373915-A-G		not specified	Uncertain significance (Jun 17, 2024)
20-45373995-G-A		not specified	Likely benign (Apr 04, 2024)
20-45375061-A-G		not specified	Uncertain significance (Jun 19, 2024)
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)
20-45375130-A-G		not specified	Uncertain significance (May 02, 2024)
20-45375136-C-T		not specified	Uncertain significance (Mar 01, 2023)
20-45375157-C-T		not specified	Uncertain significance (Jan 18, 2023)
20-45375203-G-C		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYS1	protein_coding	protein_coding	ENST00000243918	3	14862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0709	0.878	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.661	76	94.0	0.808	0.00000541	988
Missense in Polyphen		13	26.681	0.48723		318
Synonymous	0.0609	41	41.5	0.988	0.00000238	331
Loss of Function	1.65	3	8.05	0.373	4.31e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in protein trafficking. May serve as a receptor for ARFRP1.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.221
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.276

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sys1

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;trans-Golgi network membrane