STXBP5L

syntaxin binding protein 5L, the group of WD repeat domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:120908071-121424761

Links

ENSG00000145087 ∙ NCBI:9515 ∙ OMIM:609381 ∙ HGNC:30757 ∙ Uniprot:Q9Y2K9 ∙ 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 STXBP5L gene.

• Inborn genetic diseases (49 variants)
• not provided (5 variants)
• STXBP5L-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STXBP5L 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				1		1
missense			50	1		51
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	51	2	0

Variants in STXBP5L

This is a list of pathogenic ClinVar variants found in the STXBP5L region.

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

Position	Type	Phenotype	Significance	ClinVar
3-120909640-G-A		STXBP5L-related disorder	Uncertain significance (Apr 10, 2023)
3-120909687-G-C		not specified	Uncertain significance (Feb 16, 2023)
3-120909696-G-T		not specified	Uncertain significance (Jun 16, 2023)
3-120909706-C-T		not specified	Uncertain significance (Jul 05, 2022)
3-120909733-A-C		not specified	Uncertain significance (Mar 17, 2023)
3-120954973-G-A		not specified	Uncertain significance (May 08, 2023)
3-120955001-T-G		not specified	Uncertain significance (Dec 12, 2023)
3-120955016-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-121041722-T-A		not specified	Uncertain significance (Feb 13, 2024)
3-121045496-G-C		not specified	Uncertain significance (Feb 06, 2024)
3-121045507-C-T		not specified	Uncertain significance (Sep 01, 2021)
3-121045512-T-G		not specified	Uncertain significance (Nov 17, 2022)
3-121045520-A-G		not specified	Uncertain significance (May 03, 2023)
3-121045529-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-121114989-A-G		not specified	Uncertain significance (Jun 29, 2022)
3-121152492-G-T			Uncertain significance (Jan 21, 2016)
3-121152529-A-G		not specified	Uncertain significance (May 24, 2023)
3-121152530-A-C		not specified	Uncertain significance (Jul 20, 2021)
3-121152555-G-C		not specified	Uncertain significance (Feb 28, 2024)
3-121157584-C-A		not specified	Uncertain significance (Feb 17, 2024)
3-121157585-C-G		not specified	Uncertain significance (Nov 15, 2021)
3-121205916-TC-T			Benign (Dec 31, 2019)
3-121205946-A-G		not specified	Uncertain significance (Feb 13, 2024)
3-121223040-G-A		not specified	Uncertain significance (Nov 27, 2023)
3-121223046-G-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STXBP5L	protein_coding	protein_coding	ENST00000273666	27	516690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000742	124770	0	24	124794	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	511	632	0.809	0.0000324	7752
Missense in Polyphen		180	251.99	0.71431		3127
Synonymous	-0.228	217	213	1.02	0.0000107	2257
Loss of Function	6.32	10	64.9	0.154	0.00000355	789

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000452
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000721	0.0000706
Middle Eastern	0.000113	0.000111
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicle trafficking and exocytosis. {ECO:0000305}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.445
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.63

Haploinsufficiency Scores

• pHI: 0.252
• hipred: Y
• hipred_score: 0.554
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stxbp5l
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: exocytosis;protein transport;regulation of exocytosis;glucose homeostasis;positive regulation of GTPase activity;negative regulation of insulin secretion;regulation of synaptic vesicle exocytosis
• Cellular component: cytoplasm;plasma membrane;integral component of membrane;SNARE complex;neuromuscular junction;neuronal dense core vesicle
• Molecular function: GTPase activator activity;Rab GTPase binding;syntaxin binding