STX19

syntaxin 19, the group of Syntaxins

Basic information

Region (hg38): 3:94014365-94028597

Links

ENSG00000178750

∙ NCBI:415117 ∙ ∙ HGNC:19300 ∙ Uniprot:Q8N4C7 ∙ 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 STX19 gene.

not_specified (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001001850.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			26 clinvar	1 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX19	protein_coding	protein_coding	ENST00000315099	1	14242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.56e-7	0.168	125627	1	65	125693	0.000263

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.464	159	143	1.11	0.00000648	1961
Missense in Polyphen		46	44.538	1.0328		627
Synonymous	-1.08	56	46.6	1.20	0.00000200	515
Loss of Function	-0.0505	10	9.83	1.02	4.89e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000925	0.000921
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000655	0.000621
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role in endosomal trafficking of the epidermal growth factor receptor (EGFR). {ECO:0000250|UniProtKB:Q8R1Q0}.;
Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics (Consensus)

Intolerance Scores

loftool: 0.837
rvis_EVS: 0.26
rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

pHI: 0.196
hipred: N
hipred_score: 0.251
ghis: 0.461

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Stx19
Phenotype: homeostasis/metabolism phenotype;

Gene ontology

Biological process: intracellular protein transport;exocytosis;vesicle fusion;synaptic vesicle fusion to presynaptic active zone membrane;vesicle docking
Cellular component: plasma membrane;synaptic vesicle;endomembrane system;integral component of membrane;SNARE complex;presynaptic membrane;presynaptic active zone membrane
Molecular function: SNARE binding;SNAP receptor activity;protein binding