SYBU

syntabulin

Basic information

Region (hg38): 8:109573978-109691791

Links

ENSG00000147642 ∙ NCBI:55638 ∙ OMIM:611568 ∙ HGNC:26011 ∙ Uniprot:Q9NX95 ∙ 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 SYBU gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYBU 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			52	2	1	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	54	2	3

Variants in SYBU

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

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

Position	Type	Phenotype	Significance	ClinVar
8-109574911-T-C		not specified	Uncertain significance (Jan 03, 2024)
8-109575000-G-A		not specified	Uncertain significance (Feb 07, 2023)
8-109575018-C-G		not specified	Uncertain significance (Jul 26, 2024)
8-109575034-C-A		not specified	Uncertain significance (Jan 30, 2024)
8-109575046-C-T		not specified	Uncertain significance (Apr 17, 2024)
8-109575063-A-G			Uncertain significance (Aug 01, 2022)
8-109575106-C-T		not specified	Uncertain significance (May 26, 2024)
8-109575112-C-T		not specified	Uncertain significance (Jan 09, 2024)
8-109575124-G-C		not specified	Uncertain significance (Feb 25, 2025)
8-109575187-T-G		not specified	Uncertain significance (Jan 16, 2025)
8-109575189-G-A		not specified	Uncertain significance (Nov 12, 2024)
8-109575197-T-G		not specified	Uncertain significance (May 27, 2022)
8-109575255-G-T		not specified	Uncertain significance (Jan 06, 2023)
8-109575294-G-T		not specified	Uncertain significance (Apr 06, 2024)
8-109575303-A-G		not specified	Uncertain significance (Aug 07, 2024)
8-109575304-A-G		not specified	Uncertain significance (Feb 14, 2023)
8-109575342-G-A		not specified	Uncertain significance (Feb 10, 2023)
8-109575365-C-G		not specified	Uncertain significance (Mar 06, 2023)
8-109575395-C-A		not specified	Uncertain significance (Sep 01, 2021)
8-109575455-A-T		not specified	Uncertain significance (May 08, 2023)
8-109575505-C-T		not specified	Uncertain significance (Aug 12, 2021)
8-109575508-C-T		not specified	Uncertain significance (Sep 29, 2023)
8-109575523-C-G		not specified	Likely benign (Oct 25, 2022)
8-109575523-C-T		not specified	Uncertain significance (Mar 31, 2023)
8-109575549-G-T		not specified	Uncertain significance (May 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYBU	protein_coding	protein_coding	ENST00000422135	7	117814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000977	0.997	124775	0	30	124805	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	330	390	0.847	0.0000229	4321
Missense in Polyphen		119	160.09	0.74334		1807
Synonymous	-0.462	163	156	1.05	0.00000958	1344
Loss of Function	2.64	11	25.4	0.434	0.00000154	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000357	0.000357
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000125	0.000124
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of a kinesin motor-adapter complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. {ECO:0000250, ECO:0000269|PubMed:15459722}.

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.756
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sybu

Zebrafish Information Network

• Gene name: sybu
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: wholly ventralized

Gene ontology

• Biological process: axonal transport of mitochondrion;positive regulation of insulin secretion involved in cellular response to glucose stimulus;regulation of synaptic activity;synapse maturation;anterograde neuronal dense core vesicle transport
• Cellular component: Golgi membrane;microtubule;integral component of membrane;cytoplasmic vesicle;vesicle;intracellular membrane-bounded organelle;dense body;axon cytoplasm
• Molecular function: protein binding;microtubule binding;syntaxin-1 binding;kinesin binding