SBSPON

somatomedin B and thrombospondin type 1 domain containing

Basic information

Region (hg38): 8:73064543-73124088

Previous symbols: [ "C8orf84" ]

Links

ENSG00000164764 ∙ NCBI:157869 ∙ ∙ HGNC:30362 ∙ Uniprot:Q8IVN8 ∙ 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 SBSPON gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBSPON 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		1
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in SBSPON

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

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

Position	Type	Phenotype	Significance	ClinVar
8-73067359-G-C		not specified	Uncertain significance (Dec 03, 2024)
8-73067366-G-A		not specified	Uncertain significance (Dec 28, 2022)
8-73067394-G-A		not specified	Uncertain significance (Dec 19, 2022)
8-73067421-G-A		not specified	Uncertain significance (Dec 26, 2023)
8-73069874-A-G		not specified	Uncertain significance (Jan 05, 2022)
8-73069883-G-A		not specified	Uncertain significance (Jun 01, 2023)
8-73069922-G-C		not specified	Uncertain significance (Feb 06, 2024)
8-73069959-C-G		not specified	Uncertain significance (Jun 02, 2023)
8-73069967-A-G		not specified	Uncertain significance (Nov 27, 2024)
8-73069980-A-T		not specified	Uncertain significance (Oct 06, 2021)
8-73071787-C-T		not specified	Uncertain significance (Apr 14, 2022)
8-73071829-T-C		not specified	Uncertain significance (Sep 12, 2023)
8-73071865-C-T		not specified	Uncertain significance (Mar 29, 2022)
8-73071870-A-T		not specified	Uncertain significance (Feb 26, 2024)
8-73081032-G-A			Likely benign (Apr 01, 2023)
8-73081082-C-T		not specified	Uncertain significance (Jan 23, 2023)
8-73081106-C-T		not specified	Uncertain significance (Jun 22, 2023)
8-73081132-C-T		not specified	Uncertain significance (Jan 09, 2024)
8-73081133-G-A		not specified	Uncertain significance (Nov 25, 2024)
8-73081139-G-A		not specified	Uncertain significance (Jun 23, 2023)
8-73081148-T-C		not specified	Likely benign (Dec 28, 2023)
8-73081192-T-A		not specified	Uncertain significance (Feb 05, 2024)
8-73081207-G-A		not specified	Uncertain significance (Dec 06, 2022)
8-73092892-G-A		not specified	Uncertain significance (May 09, 2022)
8-73092938-C-G		not specified	Uncertain significance (Sep 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SBSPON	protein_coding	protein_coding	ENST00000297354	5	59549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000671	0.728	124739	0	56	124795	0.000224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0552	155	153	1.01	0.00000888	1691
Missense in Polyphen		59	59.251	0.99576		661
Synonymous	-0.304	59	56.1	1.05	0.00000336	501
Loss of Function	1.12	10	14.6	0.683	8.11e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000873	0.000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.000534	0.000501
Finnish	0.00	0.00
European (Non-Finnish)	0.000208	0.000203
Middle Eastern	0.000534	0.000501
South Asian	0.000439	0.000425
Other	0.000172	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.197
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sbspon

Gene ontology

• Biological process: receptor-mediated endocytosis;immune response
• Cellular component: collagen-containing extracellular matrix
• Molecular function: scavenger receptor activity;extracellular matrix structural constituent;polysaccharide binding