STXBP6

syntaxin binding protein 6

Basic information

Region (hg38): 14:24809454-25050147

Links

ENSG00000168952 ∙ ∙ OMIM:607958 ∙ HGNC:19666 ∙ Uniprot:Q8NFX7 ∙ 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 STXBP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STXBP6 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in STXBP6

This is a list of pathogenic ClinVar variants found in the STXBP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24812726-T-C		not specified	Uncertain significance (Oct 07, 2024)
14-24819101-C-T		not specified	Uncertain significance (Dec 03, 2021)
14-24819132-C-A		not specified	Uncertain significance (Nov 14, 2024)
14-24819153-C-T		not specified	Uncertain significance (Jun 02, 2023)
14-24855938-C-T		not specified	Uncertain significance (Aug 10, 2024)
14-24856007-T-A		not specified	Uncertain significance (Apr 05, 2023)
14-24856040-G-A		not specified	Uncertain significance (Mar 29, 2023)
14-24856097-G-A		not specified	Uncertain significance (Nov 09, 2021)
14-24857103-C-G		not specified	Uncertain significance (Jul 09, 2021)
14-24857133-G-A		not specified	Uncertain significance (Jul 26, 2022)
14-24974749-G-C		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STXBP6	protein_coding	protein_coding	ENST00000323944	5	240642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000787	0.775	125721	0	15	125736	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.711	94	116	0.814	0.00000633	1381
Missense in Polyphen		21	27.259	0.77038		322
Synonymous	-0.113	45	44.0	1.02	0.00000272	374
Loss of Function	1.12	8	12.2	0.654	6.90e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000587	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.0000587	0.0000544
South Asian	0.0000686	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms non-fusogenic complexes with SNAP25 and STX1A and may thereby modulate the formation of functional SNARE complexes and exocytosis.

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.512
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.234
• hipred: Y
• hipred_score: 0.719
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stxbp6

Gene ontology

• Biological process: exocytosis;Golgi to plasma membrane transport;regulation of SNARE complex assembly;negative regulation of exocytosis;exocyst localization;cell-cell adhesion
• Cellular component: exocyst;plasma membrane;cell-cell adherens junction;integral component of membrane
• Molecular function: phosphatidylinositol-4,5-bisphosphate binding;GTP-Rho binding;cadherin binding involved in cell-cell adhesion