SCUBE1
Basic information
Region (hg38): 22:43197280-43343372
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (152 variants)
- not_provided (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCUBE1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173050.5. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 6 | |||||
missense | 147 | 153 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 147 | 7 | 5 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SCUBE1 | protein_coding | protein_coding | ENST00000360835 | 22 | 146106 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.961 | 0.0392 | 125723 | 0 | 25 | 125748 | 0.0000994 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.98 | 496 | 636 | 0.779 | 0.0000423 | 6479 |
Missense in Polyphen | 180 | 266.52 | 0.67537 | 2701 | ||
Synonymous | -0.353 | 276 | 269 | 1.03 | 0.0000206 | 1833 |
Loss of Function | 5.56 | 10 | 54.2 | 0.185 | 0.00000268 | 600 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000151 | 0.000151 |
Ashkenazi Jewish | 0.000128 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000930 | 0.0000924 |
European (Non-Finnish) | 0.0000937 | 0.0000879 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000265 | 0.000229 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Could function as an adhesive molecule and its matrix bound and soluble fragments may play a critical role in vascular biology. {ECO:0000269|PubMed:16753137}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.0505
- rvis_EVS
- -1.45
- rvis_percentile_EVS
- 3.93
Haploinsufficiency Scores
- pHI
- 0.272
- hipred
- Y
- hipred_score
- 0.693
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.226
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scube1
- Phenotype
- craniofacial phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; embryo phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- scube1
- Affected structure
- blood cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- inflammatory response;adult heart development;blood coagulation;post-embryonic development;extracellular matrix disassembly;endothelial cell differentiation;positive regulation of smoothened signaling pathway;protein homooligomerization
- Cellular component
- extracellular space;plasma membrane;external side of plasma membrane;cell surface;extrinsic component of plasma membrane
- Molecular function
- calcium ion binding;identical protein binding;protein heterodimerization activity