SPON1

spondin 1

Basic information

Region (hg38): 11:13962722-14268133

Links

ENSG00000262655 ∙ NCBI:10418 ∙ OMIM:604989 ∙ HGNC:11252 ∙ Uniprot:Q9HCB6 ∙ 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 SPON1 gene.

• Inborn genetic diseases (25 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPON1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	1

Variants in SPON1

This is a list of pathogenic ClinVar variants found in the SPON1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-13962936-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-13962942-C-T		not specified	Uncertain significance (Nov 09, 2022)
11-13962978-C-T		not specified	Likely benign (Oct 05, 2022)
11-13963004-C-G		not specified	Uncertain significance (Jul 26, 2021)
11-13963029-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-13963035-G-A		not specified	Uncertain significance (May 11, 2022)
11-13963036-C-T			Benign (Dec 31, 2018)
11-13963043-A-G		not specified	Uncertain significance (Dec 20, 2023)
11-13963052-G-A		not specified	Uncertain significance (May 23, 2023)
11-13963056-A-G		not specified	Uncertain significance (Jul 27, 2022)
11-13963064-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-13963094-C-T		not specified	Uncertain significance (Dec 27, 2022)
11-13963108-C-A		not specified	Uncertain significance (Sep 25, 2023)
11-13963136-T-A		not specified	Uncertain significance (Jun 27, 2022)
11-13982870-T-A		not specified	Uncertain significance (Mar 21, 2023)
11-13982879-A-G		not specified	Uncertain significance (May 01, 2022)
11-13982903-A-G		not specified	Uncertain significance (Sep 12, 2023)
11-14041566-G-A		not specified	Uncertain significance (Jan 18, 2022)
11-14041572-A-T		not specified	Uncertain significance (Jan 23, 2023)
11-14041636-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-14075355-G-A		not specified	Uncertain significance (Jul 20, 2022)
11-14075367-A-G		not specified	Uncertain significance (Oct 29, 2021)
11-14075376-T-A		not specified	Uncertain significance (Jun 29, 2022)
11-14079992-C-T		not specified	Uncertain significance (Feb 02, 2022)
11-14080006-C-T		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion protein that promotes the attachment of spinal cord and sensory neuron cells and the outgrowth of neurites in vitro. May contribute to the growth and guidance of axons in both the spinal cord and the PNS (By similarity). Major factor for vascular smooth muscle cell. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.235

Haploinsufficiency Scores

• pHI: 0.671
• ghis: 0.428

Mouse Genome Informatics

• Gene name: Spon1
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: cell adhesion;positive regulation of protein processing;positive regulation of protein binding;negative regulation of amyloid-beta formation;positive regulation of amyloid precursor protein catabolic process
• Cellular component: extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding;metal ion binding;LBD domain binding