SPON1

spondin 1

Basic information

Region (hg38): 11:13962723-14268133

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.

not_specified (57 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. These statistics are base on transcript: NM_000006108.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			56 clinvar	1 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	56	1	0

Loading clinvar variants...

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
hipred
hipred_score
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