STBD1

starch binding domain 1

Basic information

Region (hg38): 4:76306733-76311130

Links

ENSG00000118804 ∙ NCBI:8987 ∙ OMIM:607406 ∙ HGNC:24854 ∙ Uniprot:O95210 ∙ 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 STBD1 gene.

• not_specified (52 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STBD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003943.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			51	1		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STBD1	protein_coding	protein_coding	ENST00000237642	2	59867

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.66e-12	0.0103	125331	2	415	125748	0.00166

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.228	182	191	0.954	0.00000874	2346
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00283	0.00283
Ashkenazi Jewish	0.0148	0.0148
East Asian	0.000707	0.000707
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.00117	0.00117
Middle Eastern	0.000707	0.000707
South Asian	0.000556	0.000523
Other	0.00407	0.00408

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Exercise-induced Circadian Regulation;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0620

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.0508
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0735

Mouse Genome Informatics

• Gene name: Stbd1

Gene ontology

• Biological process: glycogen catabolic process;neutrophil degranulation;intracellular transport;glycophagy
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;plasma membrane;integral component of plasma membrane;membrane;T-tubule;phagophore assembly site membrane;perinuclear region of cytoplasm;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: protein binding;enzyme binding;polysaccharide binding;glycogen binding;starch binding