SPON2

spondin 2

Basic information

Region (hg38): 4:1166932-1208962

Links

ENSG00000159674 ∙ NCBI:10417 ∙ OMIM:605918 ∙ HGNC:11253 ∙ Uniprot:Q9BUD6 ∙ 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 SPON2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPON2 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	2	4
missense			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1		1
Total	0	0	39	4	2

Variants in SPON2

This is a list of pathogenic ClinVar variants found in the SPON2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-1167496-C-G		not specified	Uncertain significance (Aug 30, 2021)
4-1167501-C-T		not specified	Uncertain significance (Jan 08, 2024)
4-1167506-T-A		not specified	Uncertain significance (Sep 22, 2022)
4-1167570-T-G		not specified	Uncertain significance (May 30, 2024)
4-1167607-T-C			Benign (May 22, 2018)
4-1167608-C-G		not specified	Uncertain significance (Jun 07, 2024)
4-1167623-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-1167645-G-A		not specified	Uncertain significance (Jun 27, 2022)
4-1167654-G-A		not specified	Uncertain significance (Nov 09, 2023)
4-1167660-G-A			Benign (Dec 04, 2017)
4-1167666-G-A			Likely benign (May 22, 2018)
4-1170393-GTC-G			Likely benign (Nov 01, 2023)
4-1170431-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-1170434-C-T		not specified	Uncertain significance (Jul 26, 2024)
4-1170450-C-T		not specified	Uncertain significance (Feb 27, 2024)
4-1170451-G-A			Likely benign (Jul 01, 2022)
4-1170500-C-T		not specified	Uncertain significance (Mar 07, 2024)
4-1170520-C-T			Benign (Dec 04, 2017)
4-1170528-G-A		not specified	Uncertain significance (Jan 10, 2023)
4-1170537-A-G		not specified	Uncertain significance (May 09, 2024)
4-1170566-G-A		not specified	Uncertain significance (Sep 30, 2024)
4-1171028-C-A		not specified	Uncertain significance (Jan 06, 2023)
4-1171042-G-A		not specified	Uncertain significance (May 13, 2024)
4-1171044-G-C		not specified	Uncertain significance (Jul 19, 2022)
4-1171059-G-T		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPON2	protein_coding	protein_coding	ENST00000290902	5	42031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.66e-15	0.00131	125680	0	60	125740	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.810	233	201	1.16	0.0000106	2084
Missense in Polyphen		68	59.738	1.1383		621
Synonymous	-1.79	116	93.9	1.23	0.00000531	695
Loss of Function	-1.43	19	13.3	1.42	6.59e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000271
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000894	0.000870
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000212	0.000202
Middle Eastern	0.000894	0.000870
South Asian	0.000395	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion protein that promotes adhesion and outgrowth of hippocampal embryonic neurons. Binds directly to bacteria and their components and functions as an opsonin for macrophage phagocytosis of bacteria. Essential in the initiation of the innate immune response and represents a unique pattern- recognition molecule in the ECM for microbial pathogens (By similarity). Binds bacterial lipopolysaccharide (LPS). {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation;Beta2 integrin cell surface interactions (Consensus)

Intolerance Scores

• loftool: 0.755
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.184
• hipred: N
• hipred_score: 0.275
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spon2
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: mast cell mediated immunity;cell adhesion;axon guidance;opsonization;positive regulation of interleukin-6 production;positive regulation of tumor necrosis factor production;induction of bacterial agglutination;innate immune response;defense response to fungus;defense response to virus;positive regulation of macrophage cytokine production;cellular response to lipopolysaccharide
• Cellular component: extracellular matrix;extracellular exosome
• Molecular function: lipopolysaccharide binding;antigen binding;protein binding;metal ion binding