STXBP5L syntaxin binding protein 5L [Homo sapiens (human)] - Gene

Summary

Official Symbol: STXBP5Lprovided by HGNC
Official Full Name: syntaxin binding protein 5Lprovided by HGNC
Primary source: HGNC:HGNC:30757
See related: Ensembl:ENSG00000145087 MIM:609381; AllianceGenome:HGNC:30757
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LLGL4
Summary: The protein encoded by this gene is similar to syntaxin-binding protein 5 and contains ten N-terminal WD40 repeats, four variable region WD40 repeats, and a C-terminal R-SNARE domain. Studies of the orthologous proteins in mouse and rat have shown that the encoded protein may inhibit exocytosis in neurosecretory cells, and may negatively regulate the secretion of insulin. A missense variant in this gene is likely the cause of an infantile-onset neurodegenerative disorder diagnosed in two siblings of consanguineous parents. [provided by RefSeq, Jan 2017]
Expression: Biased expression in brain (RPKM 4.6), thyroid (RPKM 3.2) and 5 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q13.33

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (120908205..121424761)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (123628071..124144685)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (120627052..121143608)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
Title: Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
Homozygous mutation of STXBP5L is associated with autosomal recessive infantile-onset neurodegenerative disorder.
Title: Homozygous mutation of STXBP5L explains an autosomal recessive infantile-onset neurodegenerative disorder.
A homozygous nonsynonymous mutation in STXBP5L (c.3127G>A, p.Val1043Ile [CCDS43137.1]) was implicated in an infantile-onset neurodegenerative disorder manifesting a predominant sensorimotor axonal neuropathy, optic atrophy and cognitive deficit.
Title: Homozygous mutation of STXBP5L explains an autosomal recessive infantile-onset neurodegenerative disorder.
In skin aging rs322458, was in linkage disequilibrium (LD) with intronic single nucleotide polymorphisms of the STXBP5L gene, which is expressed in the skin.
Title: A genome-wide association study in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: Multiple variants in toll-like receptor 4 gene modulate risk of liver fibrosis in Caucasians with chronic hepatitis C infection.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-154102 (e-PCR)
- UniSTS:177983

SHGC-85203 (e-PCR)
- UniSTS:104043

A006Y27 (e-PCR)
- UniSTS:21869

D3S2916E (e-PCR)
- UniSTS:150900

D3S3023 (e-PCR)
- UniSTS:45459

SHGC-109993 (e-PCR)
- UniSTS:170148

STXBP5L__5348 (e-PCR)
- UniSTS:464575

WI-21827 (e-PCR)
- UniSTS:16068

SHGC-153705 (e-PCR)
- UniSTS:177895

DXS6736 (e-PCR)
- UniSTS:16872

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables myosin II binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Golgi to plasma membrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: syntaxin-binding protein 5-like

Names: lethal(2) giant larvae protein homolog 4; syntaxin binding protein 5 like; tomosyn-2; tomosyn-like

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_052890.1 RefSeqGene

Range

5003..521559

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001308330.2 → NP_001295259.1 syntaxin-binding protein 5-like isoform 2

See identical proteins and their annotated locations for NP_001295259.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1. Variants 2, 4, and 5 all encode the same isoform (2).

Source sequence(s)

AC078854, AC079841, AI279148, AK296544

Consensus CDS

CCDS77799.1

UniProtKB/TrEMBL

B4DKF6, E9PFI2

Related

ENSP00000420019.1, ENST00000471454.6

Conserved Domains (5) summary

COG2319
Location:249 → 552

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1095 → 1155

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

pfam08366
Location:288 → 396

LLGL; LLGL2

cl29593
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001348343.2 → NP_001335272.1 syntaxin-binding protein 5-like isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (1).

Source sequence(s)

AC072026, AC078854, AC078857, AC079841, AC128659

Consensus CDS

CCDS43137.1

UniProtKB/Swiss-Prot

Q4G1B4, Q6PIC3, Q9Y2K9

UniProtKB/TrEMBL

B4DKF6

Related

ENSP00000516710.1, ENST00000707001.1

Conserved Domains (5) summary

COG2319
Location:249 → 552

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1119 → 1179

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

pfam08366
Location:288 → 396

LLGL; LLGL2

cl29593
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001348344.2 → NP_001335273.1 syntaxin-binding protein 5-like isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1. Variants 2, 4, and 5 all encode the same isoform (2).

Source sequence(s)

AC072026, AC078854, AC078857, AC079841, AC128659

Consensus CDS

CCDS77799.1

UniProtKB/TrEMBL

B4DKF6, E9PFI2

Conserved Domains (5) summary

COG2319
Location:249 → 552

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1095 → 1155

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

pfam08366
Location:288 → 396

LLGL; LLGL2

cl29593
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001348345.2 → NP_001335274.1 syntaxin-binding protein 5-like isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1. Variants 2, 4, and 5 all encode the same isoform (2).

Source sequence(s)

AC072026, AC078854, AC078857, AC079841, AC128659

Consensus CDS

CCDS77799.1

UniProtKB/TrEMBL

B4DKF6, E9PFI2

Conserved Domains (5) summary

COG2319
Location:249 → 552

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1095 → 1155

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

pfam08366
Location:288 → 396

LLGL; LLGL2

cl29593
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_014980.3 → NP_055795.1 syntaxin-binding protein 5-like isoform 1

See identical proteins and their annotated locations for NP_055795.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 3 both encode the same isoform (1).

Source sequence(s)

AB023223, AC079841, AI279148, DC324331

Consensus CDS

CCDS43137.1

UniProtKB/Swiss-Prot

Q4G1B4, Q6PIC3, Q9Y2K9

UniProtKB/TrEMBL

B4DKF6

Related

ENSP00000273666.6, ENST00000273666.10

Conserved Domains (5) summary

COG2319
Location:249 → 552

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1119 → 1179

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

pfam08366
Location:288 → 396

LLGL; LLGL2

cl29593
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

NR_145516.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC072026, AC078854, AC078857, AC079841, AC128659
NR_145517.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) is shorter at the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC072026, AC078857, AC128659

Related

ENST00000461772.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

120908205..121424761

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017007534.2 → XP_016863023.1 syntaxin-binding protein 5-like isoform X3
XM_011513331.3 → XP_011511633.1 syntaxin-binding protein 5-like isoform X4

Conserved Domains (4) summary

COG2319
Location:109 → 494

WD40; WD40 repeat [General function prediction only]

pfam08366
Location:289 → 396

LLGL; LLGL2

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

cl02567
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_011513333.4 → XP_011511635.1 syntaxin-binding protein 5-like isoform X6

Conserved Domains (4) summary

COG2319
Location:109 → 494

WD40; WD40 repeat [General function prediction only]

pfam08366
Location:289 → 396

LLGL; LLGL2

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

cl02567
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_006713825.4 → XP_006713888.1 syntaxin-binding protein 5-like isoform X1

See identical proteins and their annotated locations for XP_006713888.1

UniProtKB/Swiss-Prot

Q4G1B4, Q6PIC3, Q9Y2K9

UniProtKB/TrEMBL

B4DKF6

Conserved Domains (5) summary

COG2319
Location:249 → 552

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1119 → 1179

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

pfam08366
Location:288 → 396

LLGL; LLGL2

cl29593
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_017007535.3 → XP_016863024.1 syntaxin-binding protein 5-like isoform X6

Conserved Domains (4) summary

COG2319
Location:109 → 494

WD40; WD40 repeat [General function prediction only]

pfam08366
Location:289 → 396

LLGL; LLGL2

sd00039
Location:74 → 107

7WD40; WD40 repeat [structural motif]

cl02567
Location:74 → 281

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047449249.1 → XP_047305205.1 syntaxin-binding protein 5-like isoform X2
XM_011513332.2 → XP_011511634.1 syntaxin-binding protein 5-like isoform X5

Conserved Domains (1) summary

cd15893
Location:635 → 695

R-SNARE_STXBP5; SNARE domain of STXBP5

RNA

XR_924217.3 RNA Sequence
XR_001740373.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

123628071..124144685

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348472.1 → XP_054204447.1 syntaxin-binding protein 5-like isoform X3
XM_054348473.1 → XP_054204448.1 syntaxin-binding protein 5-like isoform X4
XM_054348475.1 → XP_054204450.1 syntaxin-binding protein 5-like isoform X6
XM_054348470.1 → XP_054204445.1 syntaxin-binding protein 5-like isoform X1

UniProtKB/Swiss-Prot

Q4G1B4, Q6PIC3, Q9Y2K9
XM_054348476.1 → XP_054204451.1 syntaxin-binding protein 5-like isoform X6
XM_054348471.1 → XP_054204446.1 syntaxin-binding protein 5-like isoform X2
XM_054348474.1 → XP_054204449.1 syntaxin-binding protein 5-like isoform X5