SPP2

secreted phosphoprotein 2

Basic information

Region (hg38): 2:234050679-234077134

Links

ENSG00000072080 ∙ NCBI:6694 ∙ OMIM:602637 ∙ HGNC:11256 ∙ Uniprot:Q13103 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Limited), mode of inheritance: AD
• retinitis pigmentosa (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPP2 gene.

• not_provided (178 variants)
• not_specified (28 variants)
• Retinal_dystrophy (15 variants)
• SPP2-related_disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006944.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	35	1	37
missense		1	82	11	2	96
nonsense			6			6
start loss						0
frameshift		1	3			4
splice donor/acceptor (+/-2bp)			8			8
Total	0	2	100	46	3

Highest pathogenic variant AF is 6.8409184e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPP2	protein_coding	protein_coding	ENST00000168148	7	26456

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-14	0.00202	125707	0	40	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.389	136	124	1.10	0.00000691	1398
Missense in Polyphen		35	31.191	1.1221		369
Synonymous	0.00698	44	44.1	0.999	0.00000263	362
Loss of Function	-1.37	18	12.7	1.41	5.35e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000630	0.000630
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could coordinate an aspect of bone turnover. {ECO:0000250}.
• Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.814
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.0358
• hipred: N
• hipred_score: 0.123
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00449

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spp2

Gene ontology

• Biological process: skeletal system development;platelet degranulation;negative regulation of endopeptidase activity;post-translational protein modification;cellular protein metabolic process;bone remodeling
• Cellular component: extracellular region;endoplasmic reticulum lumen;platelet dense granule lumen;collagen-containing extracellular matrix
• Molecular function: endopeptidase inhibitor activity