STX6

protein-coding

syntaxin 6, the group of Syntaxins

Gene summary

Predicted to enable SNAP receptor activity and SNARE binding activity. Involved in regulation of protein localization; retrograde transport, endosome to Golgi; and vesicle fusion. Acts upstream of or within endocytic recycling. Located in early endosome; perinuclear region of cytoplasm; and trans-Golgi network. Part of SNARE complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_005819.6

Inheritance

—

ClinVar variants

U:45B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr1:180,972,712-181,023,121

External References & Databases

Ensembl (ENSG00000135823)

Transcript & Mutation Effects

hg38 • Region Span ~50.4 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 STX6 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 40

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005819.6. 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			2 clinvar	1 clinvar		3
missense			41 clinvar	1 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	45	2	0	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005819.6	RefSeq	NP_005810.1	8	MANE Select
ENST00000258301.6	Ensembl	ENSP00000258301.5	8	MANE Select
NM_001286210.2	RefSeq	NP_001273139.1	5	Standard
ENST00000542060.5	Ensembl	ENSP00000440188.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

SNARE interactions in vesicular transport - Homo sapiens (human)
Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics
Vesicle-mediated transport
Membrane Trafficking
Intra-Golgi traffic

Biological Process

intracellular protein transport
vesicle fusion
endosome organization
synaptic vesicle to endosome fusion
endocytic recycling

Molecular Function

SNARE binding
SNAP receptor activity
protein binding
syntaxin binding

Cellular Component

Golgi membrane
nucleoplasm
early endosome
Golgi apparatus
trans-Golgi network

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258301
Coding exons: 8
Length: 50187
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125748
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.434	129	144	0.898	0.00000786	1682
Missense (PolyPhen)		42	46.885	0.89582		595
Synonymous	0.0288	50	50.3	0.995	0.00000263	463
Loss of Function	2.29	6	15.8	0.379	7.61e-7	171

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in intracellular vesicle trafficking.;

Recessive Scores

pRec: 0.170

Intolerance Scores

LoFtool: 0.226
RVIS EVS: -0.54
RVIS percentile EVS: 20.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.934

Gene Damage Prediction

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