STX12

syntaxin 12, the group of Syntaxins

Basic information

Region (hg38): 1:27773218-27824443

Links

ENSG00000117758 ∙ NCBI:23673 ∙ OMIM:606892 ∙ HGNC:11430 ∙ Uniprot:Q86Y82 ∙ 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 STX12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX12 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	14	1	0

Variants in STX12

This is a list of pathogenic ClinVar variants found in the STX12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27773318-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-27773336-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-27773350-T-G		not specified	Uncertain significance (Nov 18, 2021)
1-27773410-C-T		not specified	Uncertain significance (Dec 02, 2022)
1-27793533-G-T		not specified	Likely benign (Mar 08, 2024)
1-27793585-C-G		not specified	Uncertain significance (Dec 30, 2023)
1-27793591-G-C		not specified	Uncertain significance (Feb 17, 2023)
1-27812172-G-C		not specified	Uncertain significance (Oct 06, 2021)
1-27812184-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-27812258-G-A		not specified	Uncertain significance (May 26, 2024)
1-27819653-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-27819688-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-27819695-G-A		not specified	Uncertain significance (Jun 30, 2022)
1-27819716-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-27822237-T-A		not specified	Uncertain significance (Jan 22, 2024)
1-27822240-C-T		not specified	Uncertain significance (May 31, 2022)
1-27822255-A-G		not specified	Uncertain significance (May 10, 2024)
1-27822316-A-C		not specified	Likely benign (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX12	protein_coding	protein_coding	ENST00000373943	9	51270

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0438	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.946	116	148	0.782	0.00000759	1808
Missense in Polyphen		14	34.73	0.40311		448
Synonymous	0.718	48	54.8	0.877	0.00000278	487
Loss of Function	3.57	2	18.6	0.107	8.74e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi network. The SNARE complex containing STX6, STX12, VAMP4 and VTI1A mediates vesicle fusion (in vitro) (By similarity). Through complex formation with GRIP1, GRIA2 and NSG1 controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:G3V7P1}.
• Pathway: Phagosome - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.487
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.614
• hipred: Y
• hipred_score: 0.699
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx12

Gene ontology

• Biological process: autophagosome assembly;intracellular protein transport;vesicle fusion;cholesterol efflux;vesicle docking;protein stabilization
• Cellular component: Golgi membrane;phagophore assembly site;synaptic vesicle;endomembrane system;integral component of membrane;integral component of synaptic vesicle membrane;BLOC-1 complex;SNARE complex;early endosome membrane;vesicle;membrane raft;phagocytic vesicle;recycling endosome membrane;postsynaptic recycling endosome
• Molecular function: SNARE binding;SNAP receptor activity;protein binding