STBD1 starch binding domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: STBD1provided by HGNC
Official Full Name: starch binding domain 1provided by HGNC
Primary source: HGNC:HGNC:24854
See related: Ensembl:ENSG00000118804 MIM:607406; AllianceGenome:HGNC:24854
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GENEX3414; GENX-3414
Summary: Enables enzyme binding activity and glycogen binding activity. Involved in glycophagy and intracellular transport. Located in T-tubule; endoplasmic reticulum; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in fat (RPKM 72.0), liver (RPKM 33.4) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q21.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (76306733..76311130)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (79647451..79651849)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (77227886..77232283)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1.
Title: Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1.
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer.
Title: Model-based analysis uncovers mutations altering autophagy selectivity in human cancer.
results demonstrate that Stbd1 plays a dominant role in glycogen transport to lysosomes in liver and that the N-terminal transmembrane region and the C-terminal CBM20 domain are critical for this function.
Title: Starch Binding Domain-containing Protein 1 Plays a Dominant Role in Glycogen Transport to Lysosomes in Liver.
Atg8 interacting motif (AIM) in Stbd1 is necessary for GABARAPL1 binding.
Title: Starch-binding domain-containing protein 1 (Stbd1) and glycogen metabolism: Identification of the Atg8 family interacting motif (AIM) in Stbd1 required for interaction with GABARAPL1.

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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
Genome-wide association study reveals genetic risk underlying Parkinson's disease. 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-63501 (e-PCR)
- UniSTS:48923

D15S1477 (e-PCR)
- UniSTS:474482

SHGC-63500 (e-PCR)
- UniSTS:95397

D4S2479E (e-PCR)
- UniSTS:56756

WI-17734 (e-PCR)
- UniSTS:69045

SHGC-133062 (e-PCR)
- UniSTS:170996

Readthrough FAM47E-STBD1

Readthrough gene: FAM47E-STBD1, Included gene: FAM47E

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cargo receptor activity	IEA Inferred from Electronic Annotation more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables glycogen binding	IDA Inferred from Direct Assay more info	PubMed
enables polysaccharide binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables starch binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in glycogen catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glycophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular transport	IGI Inferred from Genetic Interaction more info	PubMed
involved_in substrate localization to autophagosome	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in phagophore assembly site membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in tertiary granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: starch-binding domain-containing protein 1

Names: genethonin 1; glycophagy cargo receptor STBD1

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.

mRNA and Protein(s)

NM_003943.5 → NP_003934.1 starch-binding domain-containing protein 1

See identical proteins and their annotated locations for NP_003934.1

Status: VALIDATED

Source sequence(s)

AK123795, BC022301

Consensus CDS

CCDS3578.1

UniProtKB/Swiss-Prot

B3KVZ9, O95210

Related

ENSP00000237642.6, ENST00000237642.7

Conserved Domains (1) summary

cd05813
Location:264 → 358

CBM20_genethonin_1; Genethonin-1, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Genethonin-1 is a human skeletal muscle protein with no known function. It contains a C-terminal CBM20 domain. The CBM20 domain is found in a large number of starch ...