SPP2

Chr 2

secreted phosphoprotein 2

Also known as: SPP-24, SPP24

NCBI Gene: 6694ENSG00000072080UniProt: Q13103

This gene encodes a secreted phosphoprotein that is a member of the cystatin superfamily. [provided by RefSeq, Oct 2008]

Research Assistant →
0
Active trials
7
Pubs (1 yr)
0
P/LP submissions
—
P/LP missense
1.89
LOEUF
DN
Mechanism· G2P
Clinical Summary— SPP2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — SPP2
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.89LOEUF
pLI 0.000
Z-score -1.37
OE 1.41 (0.97–1.89)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.39Z-score
OE missense 1.10 (0.95–1.27)
136 obs / 123.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.41 (0.97–1.89)
0≤0.351.4
Missense OE1.10 (0.95–1.27)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 18 / 12.7Missense obs/exp: 136 / 123.8Syn Z: 0.01
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
limitedSPP2-related retinitis pigmentosaDNAD
DN
0.75top 25%
GOF
0.3491th %ile
LOF
0.3355th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SPP2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Antibodies against polysaccharide type 3 and pneumococcal proteins demonstrate synergistic protective effect in a highly virulent type 3 invasive disease model in mice.
Stevenson TC et al.·Front Immunol
2025Functional
Targeting Sphingosine-1-Phosphate Signaling in Immune-Mediated Diseases: Beyond Multiple Sclerosis
Pérez-Jeldres T et al.·Drugs
2021
Integrative transcriptomic and metabolomic analysis reveals the flavor formation mechanism of green bamboo (Dendrocalamopsis oldhami) shoots
Liu Y et al.·Food Chem (Oxf)
2025Functional
Potential ameliorative role of Spirulina platensis in powdered or extract forms against cyclic heat stress in broiler chickens
Elbaz AM et al.·Environ Sci Pollut Res Int
2022
Biochemical and Genetic Evidence Supports Fyv6 as a Second-Step Splicing Factor in Saccharomyces cerevisiae
Lipinski KA et al.·bioRxiv
2023
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients