SPP2
Chr 2secreted phosphoprotein 2
Also known as: SPP-24, SPP24
This gene encodes a secreted phosphoprotein that is a member of the cystatin superfamily. [provided by RefSeq, Oct 2008]
Clinical highlights
Interpreting a novel variant
A dominant-negative effect is the curated mechanism (Gene2Phenotype), so a variant that simply removes the protein may not be the pathogenic class here — missense variants in functional domains often carry more weight.Curated gene-level mechanism — a prior for triage, not a per-variant call.
📖
Open GeneReview ↗GeneReview available — SPP2
Authoritative clinical overview · Recommended first read
Some data sources returned errors (1)
omim: Error: OMIM fetch failed: 429
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
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)
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 to missense variation
Observed / Expected Ratios?
LoF OE?1.41 (0.97–1.89)
0≤0.351.4
Missense OE?1.10 (0.95–1.27)
0≤0.61.4
Synonymous OE?1.00
0≤1.21.6
LoF obs/exp: 18 / 12.7Missense obs/exp: 136 / 123.8Syn Z: 0.01
ClinVar Variant Classifications
0 submitted variants in 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.
External Resources
Links to major genomics databases and tools
📖
Open GeneReview ↗GeneReview available — SPP2
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools