SCUBE3
signal peptide, CUB domain and EGF like domain containing 3
Basic information
Region (hg38): 6:35213955-35253079
Previous symbols: [ "CEGF3" ]
Links
Phenotypes
GenCC
Source:
- short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 (Strong), mode of inheritance: AR
- short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies | AR | Cardiovascular | Among other features, the condition can involve arrhythmias, and awareness can allow early diagnosis and management | Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dental; Musculoskeletal; Neurologic | 33308444 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (36 variants)
- not provided (10 variants)
- Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 (7 variants)
- Short stature;Abnormal facial shape;Abnormality of the skeletal system;Abnormality of the dentition (6 variants)
- Abnormal facial shape;Short stature;Abnormality of the skeletal system;Abnormality of the dentition (2 variants)
- not specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCUBE3 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 41 | 48 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 1 | |||||
| Total | 7 | 1 | 42 | 1 | 4 |
Variants in SCUBE3
This is a list of pathogenic ClinVar variants found in the SCUBE3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCUBE3 | protein_coding | protein_coding | ENST00000274938 | 22 | 38667 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000614 | 125728 | 0 | 20 | 125748 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.70 | 425 | 613 | 0.693 | 0.0000371 | 6552 |
| Missense in Polyphen | 147 | 249.98 | 0.58804 | 2711 | ||
| Synonymous | 2.27 | 191 | 235 | 0.812 | 0.0000145 | 1895 |
| Loss of Function | 5.80 | 7 | 52.2 | 0.134 | 0.00000289 | 593 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000246 | 0.000242 |
| Ashkenazi Jewish | 0.000398 | 0.000397 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000441 | 0.0000439 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to TGFBR2 and activates TGFB signaling. In lung cancer cells, could serve as an endogenous autocrine and paracrine ligand of TGFBR2, which could regulate TGFBR2 signaling and hence modulate epithelial-mesenchymal transition and cancer progression. {ECO:0000269|PubMed:21441952}.;
- Pathway
- Extracellular matrix organization;Degradation of the extracellular matrix
(Consensus)
Recessive Scores
- pRec
- 0.0910
Intolerance Scores
- loftool
- 0.0393
- rvis_EVS
- -0.22
- rvis_percentile_EVS
- 37.66
Haploinsufficiency Scores
- pHI
- 0.246
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.531
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.357
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scube3
- Phenotype
- limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- extracellular matrix disassembly;positive regulation of smoothened signaling pathway;protein homooligomerization;protein heterooligomerization
- Cellular component
- extracellular space;plasma membrane;cell surface
- Molecular function
- calcium ion binding;protein binding