STXBP4

syntaxin binding protein 4, the group of PDZ domain containing

Basic information

Region (hg38): 17:54968727-55173632

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.

not_specified (65 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. These statistics are base on transcript: NM_000178509.6. 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			61 clinvar	4 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	4	0

Loading clinvar variants...

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
Phenotype

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