STBD1
protein-codingstarch binding domain 1
Gene summary
Enables enzyme binding activity and glycogen binding activity. Involved in glycophagy and lysosomal transport. Located in T-tubule; endoplasmic reticulum; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STBD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003943.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 57 | 1 | 58 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 57 | 1 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003934.1 | 2 | MANE Select | |
| Ensembl | ENSP00000237642.6 | 2 | MANE Select | |
| Ensembl | ENSP00000791507.1 | 2 | Standard | |
| Ensembl | ENSP00000794832.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Exercise-induced Circadian Regulation
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- glycogen catabolic process
- neutrophil degranulation
- intracellular transport
- glycophagy
Molecular Function
- protein binding
- enzyme binding
- polysaccharide binding
- glycogen binding
- starch binding
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- cytosol
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000237642
- Coding exons
- 2
- Length
- 59867
- Individuals with no LoFs
- 125331
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 415
- Defined
- 125748
- p
- 0.00166
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.228 | 182 | 191 | 0.954 | 0.00000874 | 2346 |
| Missense (PolyPhen) | 46 | 44.502 | 1.0337 | 574 | ||
| Synonymous | -0.298 | 76 | 72.8 | 1.04 | 0.00000341 | 714 |
| Loss of Function | -0.963 | 15 | 11.5 | 1.31 | 4.89e-7 | 138 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00093 | 0.00092 | rare |
| Latino/Admixed American | 0.0019 | 0.0019 | notable |
| Ashkenazi Jewish | 0.015 | 0.015 | notable |
| East Asian | 0.00071 | 0.00071 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.0012 | 0.0012 | notable |
| South Asian | 0.00056 | 0.00052 | rare |
| Other | 0.0041 | 0.0041 | notable |
dbNSFP Gene Annotations
Source:
- Function
- 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. {ECO:0000269|PubMed:20810658, ECO:0000269|PubMed:21893048, ECO:0000269|PubMed:24837458}.;
Recessive Scores
- pRec
- 0.0620
Intolerance Scores
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.51
Essentials
- Essential (CRISPR)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0735