SCUBE1

signal peptide, CUB domain and EGF like domain containing 1

Basic information

Region (hg38): 22:43197280-43343372

Links

ENSG00000159307 ∙ NCBI:80274 ∙ OMIM:611746 ∙ HGNC:13441 ∙ Uniprot:Q8IWY4 ∙ 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 SCUBE1 gene.

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.

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					4	4
missense			64	1	1	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	64	1	6

Variants in SCUBE1

This is a list of pathogenic ClinVar variants found in the SCUBE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43204034-C-T		not specified	Uncertain significance (May 31, 2023)
22-43204070-T-C		not specified	Uncertain significance (Sep 14, 2022)
22-43204134-T-C		not specified	Uncertain significance (Mar 29, 2022)
22-43207556-T-G		not specified	Uncertain significance (Mar 31, 2024)
22-43208156-G-A		not specified	Uncertain significance (Dec 17, 2023)
22-43208180-C-T		not specified	Uncertain significance (Sep 25, 2023)
22-43208229-G-A			Benign (May 24, 2018)
22-43210034-C-T			Benign (May 24, 2018)
22-43210142-T-C		not specified	Uncertain significance (Jul 20, 2022)
22-43210151-C-T		not specified	Uncertain significance (Jun 01, 2023)
22-43210165-G-T		not specified	Uncertain significance (Dec 22, 2023)
22-43210206-G-A			Benign (Feb 08, 2018)
22-43210232-A-C		not specified	Uncertain significance (Dec 01, 2022)
22-43210954-A-G		not specified	Uncertain significance (May 20, 2024)
22-43211006-C-T		not specified	Uncertain significance (Aug 02, 2021)
22-43211024-C-T		not specified	Uncertain significance (Sep 14, 2022)
22-43211056-T-G		not specified	Uncertain significance (May 31, 2022)
22-43212440-C-T		not specified	Uncertain significance (Dec 28, 2023)
22-43212482-C-T		not specified	Uncertain significance (Sep 17, 2021)
22-43212515-C-T		not specified	Uncertain significance (Dec 19, 2023)
22-43212554-T-C		not specified	Uncertain significance (Oct 21, 2021)
22-43214105-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-43214110-C-T		not specified	Uncertain significance (Dec 12, 2023)
22-43214125-C-T			Likely benign (May 21, 2018)
22-43214132-C-T		not specified	Uncertain significance (Nov 29, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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