STXBP4

syntaxin binding protein 4, the group of PDZ domain containing

Basic information

Region (hg38): 17:54968726-55173632

Links

ENSG00000166263 ∙ NCBI:252983 ∙ OMIM:610415 ∙ HGNC:19694 ∙ Uniprot:Q6ZWJ1 ∙ 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 STXBP4 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STXBP4 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in STXBP4

This is a list of pathogenic ClinVar variants found in the STXBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-54990825-G-T		not specified	Uncertain significance (Nov 22, 2023)
17-54990843-G-T		not specified	Uncertain significance (Jun 21, 2021)
17-54990850-A-G		not specified	Likely benign (Jul 12, 2022)
17-54990898-C-T		not specified	Uncertain significance (Nov 23, 2022)
17-54990899-G-A		not specified	Uncertain significance (Oct 22, 2021)
17-54999351-C-G		not specified	Uncertain significance (Sep 06, 2022)
17-54999352-G-A		not specified	Uncertain significance (Jun 18, 2021)
17-54999373-T-G		not specified	Uncertain significance (Mar 04, 2024)
17-54999408-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-54999751-C-T		not specified	Uncertain significance (Aug 23, 2021)
17-54999838-G-T		not specified	Likely benign (Oct 30, 2023)
17-55007506-A-C		not specified	Uncertain significance (Aug 02, 2021)
17-55007566-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-55031192-C-A		not specified	Uncertain significance (Mar 20, 2023)
17-55031239-C-G		not specified	Uncertain significance (Dec 01, 2022)
17-55047149-A-G		not specified	Uncertain significance (Feb 28, 2023)
17-55073012-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-55073044-G-C		not specified	Uncertain significance (Oct 06, 2022)
17-55073051-T-C		not specified	Uncertain significance (Jan 17, 2024)
17-55078108-A-G		not specified	Uncertain significance (Mar 02, 2023)
17-55078117-G-A		not specified	Uncertain significance (Jul 25, 2023)
17-55081103-A-G		not specified	Uncertain significance (Jan 09, 2024)
17-55081178-T-C		not specified	Uncertain significance (Mar 14, 2023)
17-55141310-G-T		not specified	Uncertain significance (Jul 11, 2022)
17-55141337-A-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STXBP4	protein_coding	protein_coding	ENST00000376352	16	195559

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.52e-14	0.227	125657	0	90	125747	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	241	275	0.875	0.0000137	3575
Missense in Polyphen		47	63.718	0.73763		851
Synonymous	1.69	74	95.0	0.779	0.00000446	1046
Loss of Function	1.15	25	32.0	0.781	0.00000152	426

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000598	0.000595
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000664	0.000653
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000329	0.000325
Middle Eastern	0.000664	0.000653
South Asian	0.000535	0.000523
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the translocation of transport vesicles from the cytoplasm to the plasma membrane. Inhibits the translocation of SLC2A4 from intracellular vesicles to the plasma membrane by STX4A binding and preventing the interaction between STX4A and VAMP2. Stimulation with insulin disrupts the interaction with STX4A, leading to increased levels of SLC2A4 at the plasma membrane. May also play a role in the regulation of insulin release by pancreatic beta cells after stimulation by glucose (By similarity). {ECO:0000250}.
• Pathway: Insulin Signaling;Insulin-mediated glucose transport;Validated transcriptional targets of deltaNp63 isoforms (Consensus)

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.880
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.251
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0386

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stxbp4

Gene ontology

• Biological process: protein targeting;cellular response to DNA damage stimulus;insulin receptor signaling pathway;regulation of glucose transmembrane transport;positive regulation of keratinocyte proliferation;protein stabilization;regulation of insulin secretion involved in cellular response to glucose stimulus;cellular response to interferon-gamma;positive regulation of cell cycle G1/S phase transition
• Cellular component: phagocytic vesicle;extracellular exosome
• Molecular function: protein binding;syntaxin binding