STXBP6

protein-coding

syntaxin binding protein 6

Gene summary

Enables cadherin binding activity involved in cell-cell adhesion. Predicted to be involved in negative regulation of exocytosis. Located in adherens junction. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001394410.1

Inheritance

—

ClinVar variants

U:24

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr14:24,809,454-25,050,147

External References & Databases

Ensembl (ENSG00000168952)

Transcript & Mutation Effects

hg38 • Region Span ~240.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STXBP6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394410.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			24 clinvar			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	0	0	24

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 118 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394410.1	RefSeq	NP_001381339.1	5	MANE Select
ENST00000323944.10	Ensembl	ENSP00000324302.5	5	MANE Select
NM_001304476.3	RefSeq	NP_001291405.1	5	Standard
NM_001304477.3	RefSeq	NP_001291406.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

exocytosis
Golgi to plasma membrane transport
regulation of SNARE complex assembly
negative regulation of exocytosis
exocyst localization

Molecular Function

phosphatidylinositol-4,5-bisphosphate binding
GTP-Rho binding
cadherin binding involved in cell-cell adhesion

Cellular Component

exocyst
plasma membrane
cell-cell adherens junction
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323944
Coding exons: 5
Length: 240642
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125736
p: 0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.711	94	116	0.814	0.00000633	1381
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000059	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000069	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.137

Gene Damage Prediction

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