STX19

Summary

STX19 (syntaxin 19, HGNC:19300) is a protein-coding gene on chromosome 3q11.2, encoding Syntaxin-19 (Q8N4C7). Plays a role in endosomal trafficking of the epidermal growth factor receptor (EGFR).

Predicted to enable SNAP receptor activity and SNARE binding activity. Predicted to be involved in intracellular protein transport; synaptic vesicle fusion to presynaptic active zone membrane; and vesicle docking. Predicted to be located in cytoplasm and membrane. Predicted to be part of SNARE complex. Predicted to be active in endomembrane system and presynaptic active zone membrane.

Source: NCBI Gene 415117 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001001850

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19300
Approved symbol	STX19
Name	syntaxin 19
Location	3q11.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC21382
Ensembl gene	ENSG00000178750
Ensembl biotype	protein_coding
Entrez	415117

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000315099, ENST00000856547, ENST00000856548, ENST00000944942, ENST00000944943, ENST00000944944

RefSeq mRNA: 1 — MANE Select: NM_001001850 NM_001001850

CCDS: CCDS33793

Canonical transcript exons

ENST00000315099 — 2 exons

Exon	Start	End
ENSE00001214978	94028367	94028597
ENSE00001214989	94014365	94015282

Expression profiles

Bgee: expression breadth ubiquitous, 176 present calls, max score 88.01.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2565 / max 25.2535, expressed in 100 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
43306	0.1552	68
43307	0.0725	34
43308	0.0289	15

Top tissues by expression

242 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	88.01	gold quality
esophagus squamous epithelium	UBERON:0006920	87.76	gold quality
rectum	UBERON:0001052	85.54	gold quality
colonic mucosa	UBERON:0000317	85.30	gold quality
palpebral conjunctiva	UBERON:0001812	83.96	gold quality
mucosa of sigmoid colon	UBERON:0004993	83.46	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.18	gold quality
gingival epithelium	UBERON:0001949	82.57	gold quality
lower esophagus mucosa	UBERON:0035834	81.42	gold quality
gingiva	UBERON:0001828	80.63	gold quality
body of pancreas	UBERON:0001150	79.19	gold quality
esophagus mucosa	UBERON:0002469	78.39	gold quality
parotid gland	UBERON:0001831	76.82	silver quality
minor salivary gland	UBERON:0001830	76.48	gold quality
saliva-secreting gland	UBERON:0001044	76.44	gold quality
mouth mucosa	UBERON:0003729	76.32	gold quality
mucosa of paranasal sinus	UBERON:0005030	76.06	gold quality
amniotic fluid	UBERON:0000173	75.28	gold quality
transverse colon	UBERON:0001157	74.95	gold quality
oral cavity	UBERON:0000167	74.03	gold quality
pancreas	UBERON:0001264	73.85	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	72.73	gold quality
skin of abdomen	UBERON:0001416	71.67	gold quality
endometrium	UBERON:0001295	71.53	gold quality
corpus epididymis	UBERON:0004359	70.78	gold quality
jejunal mucosa	UBERON:0000399	70.68	gold quality
body of stomach	UBERON:0001161	70.26	gold quality
zone of skin	UBERON:0000014	70.13	gold quality
skin of leg	UBERON:0001511	69.82	gold quality
islet of Langerhans	UBERON:0000006	69.28	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.39

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Stx19	ENSMUSG00000047854
rattus_norvegicus	Stx19	ENSRNOG00000070368
caenorhabditis_elegans		WBGENE00006371
caenorhabditis_elegans		WBGENE00006372
caenorhabditis_elegans		WBGENE00006374

Paralogs (12): STX7 (ENSG00000079950), STX1B (ENSG00000099365), STX4 (ENSG00000103496), STX1A (ENSG00000106089), STX2 (ENSG00000111450), STX12 (ENSG00000117758), STX16 (ENSG00000124222), STX11 (ENSG00000135604), STX17 (ENSG00000136874), STX5 (ENSG00000162236), STX3 (ENSG00000166900), TSNARE1 (ENSG00000171045)

Protein

Protein identifiers

Syntaxin-19 — Q8N4C7 (reviewed: Q8N4C7)

All UniProt accessions (1): Q8N4C7

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in endosomal trafficking of the epidermal growth factor receptor (EGFR).

Subunit / interactions. Interacts with EGFR.

Subcellular location. Cell membrane. Cytoplasm.

Similarity. Belongs to the syntaxin family.

RefSeq proteins (1): NP_001001850* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000727	T_SNARE_dom	Domain
IPR006011	Syntaxin_N	Domain
IPR006012	Syntaxin/epimorphin_CS	Conserved_site
IPR010989	SNARE	Homologous_superfamily
IPR045242	Syntaxin	Family

Pfam: PF00804

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4C7-F1	78.14	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, CREL_01, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_CELL_CELL_SIGNALING, GOBP_MEMBRANE_DOCKING, GOBP_EXOCYTOSIS, GOBP_VESICLE_FUSION_TO_PLASMA_MEMBRANE, GOBP_ORGANELLE_MEMBRANE_FUSION, GOBP_SECRETION, GOBP_SIGNAL_RELEASE, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION

GO Biological Process (5): intracellular protein transport (GO:0006886), exocytosis (GO:0006887), synaptic vesicle fusion to presynaptic active zone membrane (GO:0031629), obsolete vesicle docking (GO:0048278), vesicle-mediated transport (GO:0016192)

GO Molecular Function (3): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), protein binding (GO:0005515)

GO Cellular Component (6): plasma membrane (GO:0005886), endomembrane system (GO:0012505), SNARE complex (GO:0031201), presynaptic active zone membrane (GO:0048787), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
vesicle fusion to plasma membrane	2
intracellular protein localization	1
protein transport	1
intracellular transport	1
vesicle-mediated transport	1
secretion by cell	1
synaptic vesicle exocytosis	1
synaptic vesicle membrane organization	1
transport	1
cellular process	1
protein binding	1
protein-macromolecule adaptor activity	1
membrane fusion	1
fusogenic activity	1
binding	1
membrane	1
cell periphery	1
vacuole	1
plasma membrane	1
cytoplasm	1
membrane protein complex	1
presynaptic membrane	1
presynaptic active zone	1
synaptic membrane	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

795 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STX19	STXBP2	Q15833	931
STX19	SNAP23	O00161	930
STX19	UNC13D	Q70J99	870
STX19	RAB27A	P51159	777
STX19	VAMP8	Q9BV40	768
STX19	STXBP5	Q5T5C0	656
STX19	STXBP1	P61764	648
STX19	VAMP7	P51809	634
STX19	LYST	Q99698	609
STX19	PRF1	P14222	580
STX19	STXBP5L	Q9Y2K9	566
STX19	VTI1B	Q9UEU0	558
STX19	VAMP4	O75379	538
STX19	VAMP5	O95183	530
STX19	VAMP3	Q15836	526

IntAct

72 interactions, top by confidence:

A	B	Type	Score
STX19	STXBP1	psi-mi:“MI:0915”(physical association)	0.850
STXBP1	STX19	psi-mi:“MI:0915”(physical association)	0.850
STX19	STXBP1	psi-mi:“MI:0914”(association)	0.850
STX19	PRKAB2	psi-mi:“MI:0915”(physical association)	0.670
PRKAB2	STX19	psi-mi:“MI:0915”(physical association)	0.670
SYCE1	STX19	psi-mi:“MI:0915”(physical association)	0.560
STX19	SYCE1	psi-mi:“MI:0915”(physical association)	0.560
PWP2	STX19	psi-mi:“MI:0915”(physical association)	0.560
STX19	PWP2	psi-mi:“MI:0915”(physical association)	0.560
SNAP25	STX19	psi-mi:“MI:0915”(physical association)	0.560
STX19	NAPB	psi-mi:“MI:0915”(physical association)	0.560
STX19	SUFU	psi-mi:“MI:0915”(physical association)	0.560
STX19	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
STX19	ABI2	psi-mi:“MI:0915”(physical association)	0.560
STX19	ZNF330	psi-mi:“MI:0915”(physical association)	0.560
STX19	A2M	psi-mi:“MI:0915”(physical association)	0.560
STX19	CHAT	psi-mi:“MI:0915”(physical association)	0.560
STX19	DNM2	psi-mi:“MI:0915”(physical association)	0.560
STX19	FGFR3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (61): STX19 (Two-hybrid), STX19 (Two-hybrid), STX19 (Two-hybrid), STXBP1 (Affinity Capture-MS), STXBP2 (Affinity Capture-MS), PRMT3 (Affinity Capture-MS), SNAP23 (Affinity Capture-MS), SULT1A2 (Affinity Capture-MS), STXBP5L (Affinity Capture-MS), STXBP5 (Affinity Capture-MS), TBK1 (Affinity Capture-MS), VAMP3 (Affinity Capture-MS), VAMP2 (Affinity Capture-MS), ZNF277 (Affinity Capture-MS), VAMP8 (Affinity Capture-MS)

ESM2 similar proteins: A8WVD0, O15400, O16000, O35526, O70257, O70439, P32850, P32851, P32856, P32867, P39926, P50279, P61264, P61265, P61266, P61267, P61268, P70452, Q00262, Q08849, Q08850, Q0VCI2, Q12846, Q13277, Q16623, Q16932, Q20024, Q24547, Q3SWZ3, Q3ZBT5, Q42374, Q59YF0, Q5R4L2, Q5R602, Q5TX47, Q64704, Q7XIE2, Q8N4C7, Q8R1Q0, Q8VZU2

Diamond homologs: A8WVD0, O15400, O16000, O35526, O64791, O65359, O75558, O94651, P32850, P32851, P32856, P32867, P39926, P50279, P61264, P61265, P61266, P61267, P61268, P70452, Q00262, Q08144, Q08849, Q08850, Q12846, Q13277, Q16623, Q16932, Q24547, Q3SWZ3, Q3ZBT5, Q42374, Q54JY7, Q54X86, Q59YF0, Q5R4L2, Q5RAL4, Q5TX47, Q64704, Q6F3B4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

2 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

419 predictions. Top by Δscore:

Variant	Effect	Δscore
3:94015282:CCTAA:C	acceptor_loss	0.9800
3:94015283:C:CC	acceptor_gain	0.9800
3:94015283:C:CG	acceptor_loss	0.9800
3:94015284:T:G	acceptor_loss	0.9800
3:94015280:CTC:C	acceptor_gain	0.9700
3:94028362:TTTAC:T	donor_loss	0.9600
3:94028363:TTA:T	donor_loss	0.9600
3:94028364:TA:T	donor_loss	0.9600
3:94028365:A:AG	donor_loss	0.9600
3:94028366:C:CT	donor_loss	0.9600
3:94028366:CCTTT:C	donor_gain	0.9600
3:94023661:G:GA	donor_gain	0.9300
3:94027522:A:AC	donor_gain	0.9300
3:94027523:C:CC	donor_gain	0.9300
3:94028380:T:TA	donor_gain	0.9200
3:94017371:T:A	donor_gain	0.9100
3:94026879:A:T	donor_gain	0.8900
3:94016741:GGTT:G	donor_gain	0.8800
3:94015278:TCCTC:T	acceptor_gain	0.8600
3:94015279:CCTCC:C	acceptor_gain	0.8600
3:94015285:A:C	acceptor_loss	0.8600
3:94027946:GTTA:G	donor_gain	0.8600
3:94027947:TTAT:T	donor_gain	0.8600
3:94023660:T:TA	donor_gain	0.8500
3:94026880:A:AC	donor_gain	0.8500
3:94026881:C:CC	donor_gain	0.8500
3:94027519:A:AC	donor_gain	0.8500
3:94027524:A:C	donor_gain	0.8400
3:94028132:T:A	donor_gain	0.8300
3:94015281:TCCTA:T	acceptor_gain	0.8100

AlphaMissense

1971 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:94014767:C:G	R168P	0.983
3:94014966:C:G	A102P	0.980
3:94014614:A:G	L219P	0.979
3:94014644:A:G	L209P	0.979
3:94014458:G:T	A271D	0.978
3:94014761:A:G	L170P	0.977
3:94014625:T:A	R215S	0.963
3:94014625:T:G	R215S	0.963
3:94014459:C:G	A271P	0.962
3:94015012:A:C	S86R	0.956
3:94015012:A:T	S86R	0.956
3:94015014:T:G	S86R	0.956
3:94014571:G:C	F233L	0.955
3:94014571:G:T	F233L	0.955
3:94014573:A:G	F233L	0.955
3:94014688:A:C	F194L	0.955
3:94014688:A:T	F194L	0.955
3:94014690:A:G	F194L	0.955
3:94015259:C:G	R4P	0.955
3:94015247:A:G	L8P	0.954
3:94014699:A:G	W191R	0.951
3:94014699:A:T	W191R	0.951
3:94014775:A:C	F165L	0.950
3:94014775:A:T	F165L	0.950
3:94014777:A:G	F165L	0.950
3:94014575:A:G	L232P	0.934
3:94014623:T:G	H216P	0.934
3:94014626:C:G	R215T	0.930
3:94014768:G:T	R168S	0.930
3:94014753:C:G	A173P	0.929

dbSNP variants (sampled 300 via entrez): RS1000135023 (3:94016935 G>A,T), RS1000217913 (3:94026304 T>G), RS1000486203 (3:94017303 G>A,T), RS1000600441 (3:94020456 C>A,G), RS1000754263 (3:94026625 G>A,C), RS1000797888 (3:94019650 A>G), RS1000887526 (3:94026045 A>G), RS1001143754 (3:94020231 T>A), RS1001177956 (3:94028441 T>C), RS1001247204 (3:94016490 A>G), RS1001267049 (3:94023427 A>G), RS1001412648 (3:94018268 T>A), RS1001416433 (3:94029916 G>A), RS1001544968 (3:94015497 G>A,T), RS1001801810 (3:94023014 A>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:612291

GenCC curated gene-disease

Mondo (1): Joubert syndrome 8 (MONDO:0012855)

Orphanet (1): Isolated Joubert syndrome (Orphanet:475)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567358	Joubert Syndrome 8 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
Benzo(a)pyrene	affects methylation, decreases methylation	2
sodium arsenate	decreases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
avobenzone	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Lipopolysaccharides	affects response to substance, increases expression	1
Methapyrilene	increases methylation	1
Nickel	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.