STBD1

gene
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Also known as FLJ41801GENX-3414

Summary

STBD1 (starch binding domain 1, HGNC:24854) is a protein-coding gene on chromosome 4q21.1, encoding Starch-binding domain-containing protein 1 (O95210). Acts as a cargo receptor for glycogen.

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.

Source: NCBI Gene 8987 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 1 total
  • MANE Select transcript: NM_003943

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24854
Approved symbolSTBD1
Namestarch binding domain 1
Location4q21.1
Locus typegene with protein product
StatusApproved
AliasesFLJ41801, GENX-3414
Ensembl geneENSG00000118804
Ensembl biotypeprotein_coding
OMIM607406
Entrez8987

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000237642

RefSeq mRNA: 1 — MANE Select: NM_003943 NM_003943

CCDS: CCDS3578

Canonical transcript exons

ENST00000237642 — 2 exons

ExonStartEnd
ENSE000010252857630673376306989
ENSE000020240627630914476311130

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 91.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2218 / max 594.9924, expressed in 1455 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
483316.33801349
483302.4178726
483280.7298230
483290.6659201
483270.070332

Top tissues by expression

139 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
gastrocnemiusUBERON:000138891.93gold quality
muscle of legUBERON:000138391.63gold quality
skeletal muscle organUBERON:001489291.53gold quality
hindlimb stylopod muscleUBERON:000425289.18gold quality
skeletal muscle tissueUBERON:000113488.79gold quality
right lobe of liverUBERON:000111487.56gold quality
liverUBERON:000210786.10gold quality
muscle tissueUBERON:000238584.42gold quality
heart left ventricleUBERON:000208482.99gold quality
right atrium auricular regionUBERON:000663182.51gold quality
heartUBERON:000094881.99gold quality
islet of LangerhansUBERON:000000680.81gold quality
subcutaneous adipose tissueUBERON:000219080.77gold quality
adipose tissueUBERON:000101380.26gold quality
popliteal arteryUBERON:000225079.92gold quality
tibial arteryUBERON:000761079.91gold quality
apex of heartUBERON:000209879.82gold quality
left coronary arteryUBERON:000162679.44gold quality
mucosa of transverse colonUBERON:000499179.26gold quality
omental fat padUBERON:001041479.25gold quality
right coronary arteryUBERON:000162578.33gold quality
transverse colonUBERON:000115777.95gold quality
descending thoracic aortaUBERON:000234577.55gold quality
lower esophagus muscularis layerUBERON:003583377.23gold quality
lower esophagusUBERON:001347377.16gold quality
smooth muscle tissueUBERON:000113576.89gold quality
thoracic aortaUBERON:000151576.56gold quality
colonUBERON:000115576.44gold quality
ascending aortaUBERON:000149676.43gold quality
esophagogastric junction muscularis propriaUBERON:003584176.43gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no5.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting STBD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-374A-5P99.9071.342923

Literature-anchored findings (GeneRIF, showing 4)

  • Atg8 interacting motif (AIM) in Stbd1 is necessary for GABARAPL1 binding. (PMID:21893048)
  • 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. (PMID:27358407)
  • Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. (PMID:34059679)
  • Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1. (PMID:39236246)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriostbd1ENSDARG00000098408
mus_musculusStbd1ENSMUSG00000047963
rattus_norvegicusStbd1ENSRNOG00000002218

Protein

Protein identifiers

Starch-binding domain-containing protein 1O95210 (reviewed: O95210)

Alternative names: Genethonin-1, Glycophagy cargo receptor STBD1

All UniProt accessions (1): O95210

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a cargo receptor for glycogen. Delivers its cargo to an autophagic pathway called glycophagy, resulting in the transport of glycogen to lysosomes.

Subunit / interactions. Interacts with the ATG8 family proteins GABARAP and GABARAPL1. Interacts with several glycogen-associated proteins, such as GYS2 (liver glycogen synthase), GDE (glycogen debranching enzyme), GBE1 (glycogen branching enzyme 1) and EPM2A (Laforin).

Subcellular location. Preautophagosomal structure membrane. Endoplasmic reticulum membrane. Cell membrane. Sarcolemma. T-tubule.

Tissue specificity. Expressed at high level in skeletal and cardiac muscles. Moderately expressed in liver and placenta. No expression is found in pancreas, kidney or lung. Present in skeletal muscle, heart and placenta (at protein level).

Post-translational modifications. Ubiquitinated, which leads to proteasomal degradation.

Domain organisation. The LIR motif (LC3-interacting region) is required for the interaction with the ATG8 family protein GABARAPL1. The C-terminal CBM20 domain is required for the interaction with glycogen and glycogen-associated proteins.

RefSeq proteins (1): NP_003934* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002044CBM20Domain
IPR013783Ig-like_foldHomologous_superfamily
IPR013784Carb-bd-like_foldHomologous_superfamily
IPR034838CBM20_genethonin_1Domain

Pfam: PF00686

UniProt features (24 total): modified residue 9, compositionally biased region 4, mutagenesis site 3, topological domain 2, region of interest 2, chain 1, transmembrane region 1, domain 1, short sequence motif 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8X8AX-RAY DIFFRACTION1.53
8X8KX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95210-F158.440.28

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 65, 117, 148, 175, 188, 194, 210, 211, 220

Mutagenesis-validated functional residues (3):

PositionPhenotype
203abolishes interaction with gabarapl1.
206abolishes interaction with gabarapl1.
293abolishes gys2- and glycogen-binding, and leads to rapid degradation.

Function

Pathways and Gene Ontology

Reactome pathways

12 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation
R-HSA-8980692RHOA GTPase cycle
R-HSA-9013404RAC2 GTPase cycle
R-HSA-9013405RHOD GTPase cycle
R-HSA-9013408RHOG GTPase cycle
R-HSA-9013423RAC3 GTPase cycle
R-HSA-162582Signal Transduction
R-HSA-168249Innate Immune System
R-HSA-168256Immune System
R-HSA-194315Signaling by Rho GTPases
R-HSA-9012999RHO GTPase cycle
R-HSA-9716542Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 142 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_LYSOSOMAL_TRANSPORT, GOBP_VACUOLE_ORGANIZATION, GOCC_SECRETORY_GRANULE, PEREZ_TP63_TARGETS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_VACUOLAR_TRANSPORT, BROWNE_HCMV_INFECTION_16HR_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_MACROAUTOPHAGY, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GOBP_POLYSACCHARIDE_CATABOLIC_PROCESS, UEDA_PERIFERAL_CLOCK, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, TGCTGAY_UNKNOWN

GO Biological Process (7): glycogen catabolic process (GO:0005980), lysosomal transport (GO:0007041), glycophagy (GO:0061723), substrate localization to autophagosome (GO:0061753), glycogen metabolic process (GO:0005977), autophagy (GO:0006914), vesicle-mediated transport (GO:0016192)

GO Molecular Function (7): enzyme binding (GO:0019899), polysaccharide binding (GO:0030247), cargo receptor activity (GO:0038024), glycogen binding (GO:2001069), starch binding (GO:2001070), protein binding (GO:0005515), carbohydrate binding (GO:0030246)

GO Cellular Component (9): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), membrane (GO:0016020), T-tubule (GO:0030315), phagophore assembly site membrane (GO:0034045), perinuclear region of cytoplasm (GO:0048471), tertiary granule membrane (GO:0070821), ficolin-1-rich granule membrane (GO:0101003)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
RHO GTPase cycle5
Innate Immune System1
Immune System1
Signaling by Rho GTPases, Miro GTPases and RHOBTB31
Signaling by Rho GTPases1
Signal Transduction1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
polysaccharide binding2
binding2
cytoplasm2
membrane2
secretory granule membrane2
tertiary granule2
glycogen metabolic process1
glucan catabolic process1
vacuolar transport1
glycogen catabolic process1
macroautophagy1
autophagosome assembly1
establishment of localization in cell1
energy reserve metabolic process1
glucan metabolic process1
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
transport1
cellular process1
protein binding1
carbohydrate binding1
molecular_function1
vesicle-mediated transport1
molecular adaptor activity1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cell periphery1
sarcolemma1
phagophore assembly site1
ficolin-1-rich granule1

Protein interactions and networks

STRING

680 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STBD1F5GZY7F5GZY7970
STBD1GABARAPL2P60520691
STBD1CCDC62Q6P9F0616
STBD1AGLP35573613
STBD1GABARAPO95166607
STBD1EPM2AO95278605
STBD1CALCOCO2Q13137577
STBD1SQSTM1Q13501548
STBD1OPTNQ96CV9546
STBD1ACMSDQ8TDX5539
STBD1NBR1Q14596529
STBD1GYG1P46976490
STBD1GYG2O15488487
STBD1MCCC1Q96RQ3479
STBD1SYT12Q8IV01448

IntAct

48 interactions, top by confidence:

ABTypeScore
GABARAPL1STBD1psi-mi:“MI:0407”(direct interaction)0.850
STBD1GABARAPL1psi-mi:“MI:0915”(physical association)0.850
GABARAPSTBD1psi-mi:“MI:0407”(direct interaction)0.760
GABARAPSTBD1psi-mi:“MI:0915”(physical association)0.760
STBD1GABARAPpsi-mi:“MI:0914”(association)0.760
GABARAPL2IPO5psi-mi:“MI:0914”(association)0.690
STBD1GABARAPL2psi-mi:“MI:0407”(direct interaction)0.680
GABARAPL2STBD1psi-mi:“MI:0915”(physical association)0.680
GABARAPL1IPO5psi-mi:“MI:0914”(association)0.590
GABARAPIPO5psi-mi:“MI:0914”(association)0.590
KASH5STBD1psi-mi:“MI:0915”(physical association)0.560
STBD1KASH5psi-mi:“MI:0915”(physical association)0.560
MAP1LC3BSTBD1psi-mi:“MI:0407”(direct interaction)0.540
MAP1LC3BSTBD1psi-mi:“MI:0915”(physical association)0.540
KLRG2GXYLT2psi-mi:“MI:0914”(association)0.530
STBD1MID1psi-mi:“MI:0914”(association)0.530
PRKAB2STBD1psi-mi:“MI:0914”(association)0.530
PPP1R3CSTBD1psi-mi:“MI:0914”(association)0.530
PYGBSTBD1psi-mi:“MI:0914”(association)0.530
MAP1LC3ASTBD1psi-mi:“MI:0407”(direct interaction)0.440
ATF7IPSTBD1psi-mi:“MI:0915”(physical association)0.370
GABARAPL1GABARAPpsi-mi:“MI:0914”(association)0.350
GABARAPL2psi-mi:“MI:0914”(association)0.350
GABARAPL1psi-mi:“MI:0914”(association)0.350
GABARAPpsi-mi:“MI:0914”(association)0.350

BioGRID (193): CCDC155 (Two-hybrid), STBD1 (Affinity Capture-RNA), STBD1 (Affinity Capture-MS), GYG1 (Affinity Capture-MS), GYS2 (Affinity Capture-MS), GYS1 (Affinity Capture-MS), GABARAP (Affinity Capture-MS), GABARAPL1 (Affinity Capture-MS), PYGB (Affinity Capture-MS), MID1 (Affinity Capture-MS), WDFY1 (Affinity Capture-MS), GYG2 (Affinity Capture-MS), AMY1C (Affinity Capture-MS), EPM2A (Affinity Capture-MS), COL4A2 (Affinity Capture-MS)

ESM2 similar proteins: A2ALU4, A6NMK8, B1ASB6, B2RQL2, F6WEQ6, O00220, O14763, O35305, O95210, P16382, P20333, P24394, P25119, P28908, P36941, P50284, P97525, Q0VET5, Q13651, Q3TYD6, Q3U0P1, Q5PQK4, Q5SX79, Q5ZK13, Q60846, Q63257, Q66JV7, Q68CR7, Q6GQV1, Q6P1D7, Q6PHB0, Q6PJW8, Q6WG24, Q6ZRS4, Q76N32, Q80WY6, Q80XI1, Q863Z5, Q8BLK9, Q8BX35

Diamond homologs: D8Q9M3, O95210, P36914, Q2QTC2, Q5FVN1, Q6ZY51, Q8C7E7, A0A059WGE7, A0A0X1KHF9, A0A151V4J3, P22998, Q0CGA6, Q5B1W7, Q81BR3, Q9YEC5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Macroautophagy627.7×7e-06

GO biological processes:

GO termPartnersFoldFDR
autophagosome maturation556.6×2e-06
mitophagy551.3×2e-06
autophagosome assembly536.2×9e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

1 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

385 predictions. Top by Δscore:

VariantEffectΔscore
4:76309139:CTTA:Cacceptor_loss1.0000
4:76309141:TA:Tacceptor_loss1.0000
4:76309142:A:AGacceptor_gain1.0000
4:76309142:A:ATacceptor_loss1.0000
4:76309142:AG:Aacceptor_loss1.0000
4:76309143:G:GAacceptor_gain1.0000
4:76309143:G:GGacceptor_gain1.0000
4:76309143:GA:Gacceptor_gain1.0000
4:76309143:GAGC:Gacceptor_gain1.0000
4:76309133:T:Aacceptor_gain0.9900
4:76309143:GAGCA:Gacceptor_gain0.9900
4:76306987:CAGGT:Cdonor_loss0.9800
4:76306990:G:Tdonor_loss0.9800
4:76307792:C:Tdonor_gain0.9800
4:76307975:TTGAA:Tdonor_gain0.9800
4:76309141:TAGA:Tacceptor_gain0.9500
4:76308822:G:GGdonor_gain0.9400
4:76309136:T:Gacceptor_gain0.9400
4:76309142:AGAG:Aacceptor_gain0.9400
4:76309139:CTTAG:Cacceptor_gain0.9300
4:76309140:TTAG:Tacceptor_gain0.9300
4:76309141:TAG:Tacceptor_gain0.9300
4:76309142:AGA:Aacceptor_gain0.9300
4:76309143:G:Tacceptor_gain0.9300
4:76309135:A:AGacceptor_gain0.8900
4:76309140:TTAGA:Tacceptor_gain0.8800
4:76307862:G:GAdonor_gain0.8700
4:76308737:AC:Adonor_gain0.8700
4:76308821:A:AGdonor_gain0.8700
4:76306986:CCAGG:Cdonor_loss0.8500

AlphaMissense

2356 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:76309884:T:AW321R0.996
4:76309884:T:CW321R0.996
4:76309726:T:CF268S0.991
4:76309925:G:CW334C0.991
4:76309925:G:TW334C0.991
4:76309923:T:AW334R0.989
4:76309923:T:CW334R0.989
4:76309725:T:CF268L0.988
4:76309727:C:AF268L0.988
4:76309727:C:GF268L0.988
4:76309800:T:AW293R0.986
4:76309800:T:CW293R0.986
4:76309802:G:CW293C0.985
4:76309802:G:TW293C0.985
4:76309886:G:CW321C0.983
4:76309886:G:TW321C0.983
4:76309988:G:CW355C0.980
4:76309988:G:TW355C0.980
4:76309885:G:CW321S0.979
4:76309890:T:CF323L0.979
4:76309891:T:CF323S0.979
4:76309892:T:AF323L0.979
4:76309892:T:GF323L0.979
4:76309768:C:AA282E0.978
4:76309921:G:CR333P0.976
4:76309986:T:AW355R0.976
4:76309986:T:CW355R0.976
4:76309889:G:CK322N0.974
4:76309889:G:TK322N0.974
4:76306782:T:AW5R0.973

dbSNP variants (sampled 300 via entrez): RS1000182804 (4:76305194 A>T), RS1000466703 (4:76308295 T>A), RS1000786600 (4:76306677 G>A,T), RS1000859234 (4:76307716 C>T), RS1001119857 (4:76308912 A>G), RS1001302329 (4:76306470 T>C), RS1001685665 (4:76310204 GCA>G,GCACA), RS1002280214 (4:76308205 G>GTT), RS1002588633 (4:76307152 A>C,T), RS1002716351 (4:76308012 C>G,T), RS1003076957 (4:76309811 C>T), RS1003294698 (4:76308175 A>G), RS1003314024 (4:76306633 C>A,G,T), RS1004152337 (4:76307616 C>T), RS1004413064 (4:76307185 C>T)

Disease associations

OMIM: gene MIM:607406 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST000528_2Parkinson’s disease4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

52 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases expression, increases methylation4
bisphenol Adecreases expression, increases expression2
Tetrachlorodibenzodioxinincreases expression2
Cyclosporinedecreases expression, increases expression2
Aflatoxin B1affects expression, decreases expression2
Cadmium Chlorideincreases expression, decreases expression2
FR900359increases phosphorylation1
bisphenol Fincreases expression1
2,4,6-tribromophenoldecreases expression1
lasiocarpinedecreases expression1
triphenyl phosphateaffects expression1
chlortolurondecreases expression1
decabromobiphenyl etherincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
zinc chloridedecreases reaction, increases expression1
sodium arsenitedecreases expression1
cobaltous chlorideincreases expression, decreases reaction1
tetrabromobisphenol Adecreases expression1
resorcinolincreases expression1
ciglitazoneaffects binding, increases expression1
di-n-butylphosphoric acidaffects expression1
NCS 382increases expression1
CGP 52608affects binding, increases reaction1
bisphenol Bincreases expression1
abrinedecreases expression1
pentabrominated diphenyl ether 100increases expression1
hexabrominated diphenyl ether 153decreases expression1
bisphenol AFincreases expression1
Resveratrolincreases expression, affects cotreatment1
Temozolomidedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.