STX19

syntaxin 19, the group of Syntaxins

Basic information

Region (hg38): 3:94014364-94028597

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.

• Inborn genetic diseases (8 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.

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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in STX19

This is a list of pathogenic ClinVar variants found in the STX19 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-94014416-C-T		not specified	Uncertain significance (Feb 07, 2023)
3-94014513-T-C		Inborn genetic diseases	Uncertain significance (Jan 07, 2022)
3-94014527-T-C		not specified	Uncertain significance (Apr 27, 2022)
3-94014669-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-94014809-G-T		not specified	Uncertain significance (May 17, 2023)
3-94014825-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-94014846-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-94015019-C-G		not specified	Uncertain significance (Nov 17, 2023)
3-94015035-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-94015037-A-G		not specified	Uncertain significance (Feb 14, 2024)
3-94015069-A-T		not specified	Uncertain significance (Jan 05, 2022)
3-94015097-T-A		not specified	Uncertain significance (Feb 06, 2023)
3-94015187-G-A		not specified	Uncertain significance (May 15, 2023)
3-94015226-A-G		not specified	Uncertain significance (Jan 17, 2024)

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