STXBP4

syntaxin binding protein 4, the group of PDZ domain containing

Basic information

Region (hg38): 17:54968727-55173632

Links

ENSG00000166263NCBI:252983OMIM:610415HGNC:19694Uniprot:Q6ZWJ1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
STXBP4protein_codingprotein_codingENST00000376352 16195559
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.52e-140.2271256570901257470.000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7362412750.8750.00001373575
Missense in Polyphen4763.7180.73763851
Synonymous1.697495.00.7790.000004461046
Loss of Function1.152532.00.7810.00000152426

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005980.000595
Ashkenazi Jewish0.0001020.0000992
East Asian0.0006640.000653
Finnish0.0002780.000277
European (Non-Finnish)0.0003290.000325
Middle Eastern0.0006640.000653
South Asian0.0005350.000523
Other0.0001670.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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