SCUBE2

signal peptide, CUB domain and EGF like domain containing 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 11:9019476-9138114

Links

ENSG00000175356NCBI:57758OMIM:611747HGNC:30425Uniprot:Q9NQ36AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCUBE2 gene.

  • not_specified (132 variants)
  • not_provided (6 variants)
  • Cerebral_arteriovenous_malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCUBE2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001367977.2. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
1
clinvar
4
missense
1
clinvar
130
clinvar
3
clinvar
134
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 1 130 7 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCUBE2protein_codingprotein_codingENST00000520467 22118591
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.56e-210.36112543223141257480.00126
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9774825460.8820.00003066377
Missense in Polyphen246264.360.930552965
Synonymous0.8391982140.9270.00001291851
Loss of Function1.854054.80.7300.00000314618

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003040.00304
Ashkenazi Jewish0.0007940.000794
East Asian0.0004940.000489
Finnish0.0003700.000370
European (Non-Finnish)0.0008310.000827
Middle Eastern0.0004940.000489
South Asian0.003760.00370
Other0.0008160.000815

dbNSFP

Source: dbNSFP

Function
FUNCTION: Lipid-binding protein required for SHH long-range signaling by binding to the dually lipid-modified SHH (ShhNp) and by promoting ShhNp mobilization, solubilization and release from the cell membrane (PubMed:22902404, PubMed:22677548). Acts by enhancing the proteolytic processing (shedding) of the lipid- modified N- and C- terminal of ShhNp at the cell surface (PubMed:24522195). Synergizes with DISP1 to increase SHH secretion (PubMed:22902404). Probable cell surface coreceptor for VEGFR2 involved in VEGFR2-mediated angiogenesis (PubMed:27834687). {ECO:0000269|PubMed:22677548, ECO:0000269|PubMed:22902404, ECO:0000269|PubMed:24522195, ECO:0000269|PubMed:27834687, ECO:0000303|PubMed:26875496}.;
Pathway
Signal Transduction;Release of Hh-Np from the secreting cell;Hedgehog ligand biogenesis;Signaling by Hedgehog (Consensus)

Recessive Scores

pRec
0.101

Intolerance Scores

loftool
0.156
rvis_EVS
-0.7
rvis_percentile_EVS
14.81

Haploinsufficiency Scores

pHI
0.0948
hipred
N
hipred_score
0.289
ghis
0.396

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.213

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scube2
Phenotype
cellular phenotype; growth/size/body region phenotype; skeleton phenotype; limbs/digits/tail phenotype;

Zebrafish Information Network

Gene name
scube2
Affected structure
melanocyte
Phenotype tag
abnormal
Phenotype quality
irregular spatial pattern

Gene ontology

Biological process
multicellular organism development
Cellular component
extracellular region;extracellular space;cell surface
Molecular function
calcium ion binding;lipid binding