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

ENSG00000175356 ∙ NCBI:57758 ∙ OMIM:611747 ∙ HGNC:30425 ∙ Uniprot:Q9NQ36 ∙ 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 SCUBE2 gene.

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.

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				2	1	3
missense		1	54	3		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				1		1
non coding						0
Total	0	1	54	6	1

Variants in SCUBE2

This is a list of pathogenic ClinVar variants found in the SCUBE2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-9021057-T-A		not specified	Uncertain significance (Oct 22, 2021)
11-9021083-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-9021140-T-G		not specified	Uncertain significance (Dec 10, 2024)
11-9021185-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-9021188-G-A		not specified	Uncertain significance (Dec 14, 2021)
11-9021892-T-C		not specified	Uncertain significance (Jun 07, 2024)
11-9021929-T-C		not specified	Uncertain significance (Jun 07, 2024)
11-9025701-C-G			Likely benign (Dec 04, 2018)
11-9025737-G-A		not specified	Uncertain significance (Dec 22, 2023)
11-9025798-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-9027367-T-C		not specified	Uncertain significance (Apr 23, 2024)
11-9027397-C-T		not specified	Uncertain significance (Nov 09, 2024)
11-9027442-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-9027450-G-T		not specified	Uncertain significance (Feb 15, 2023)
11-9027451-G-C		not specified	Uncertain significance (May 12, 2024)
11-9027478-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-9027560-G-A			Likely benign (Dec 01, 2023)
11-9029916-A-G		not specified	Uncertain significance (Mar 21, 2024)
11-9029925-G-A		not specified	Uncertain significance (Apr 19, 2024)
11-9030003-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-9030018-T-G		not specified	Uncertain significance (Dec 01, 2022)
11-9033742-C-T		Cerebral arteriovenous malformation	Likely pathogenic (Feb 14, 2018)
11-9047367-T-C		not specified	Likely benign (Oct 03, 2022)
11-9047368-C-T			Likely benign (Mar 01, 2022)
11-9047406-C-G		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCUBE2	protein_coding	protein_coding	ENST00000520467	22	118591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.56e-21	0.361	125432	2	314	125748	0.00126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.977	482	546	0.882	0.0000306	6377
Missense in Polyphen		246	264.36	0.93055		2965
Synonymous	0.839	198	214	0.927	0.0000129	1851
Loss of Function	1.85	40	54.8	0.730	0.00000314	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00304	0.00304
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.000494	0.000489
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000831	0.000827
Middle Eastern	0.000494	0.000489
South Asian	0.00376	0.00370
Other	0.000816	0.000815

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

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