SPHKAP
Chr 2SPHK1 interactor, AKAP domain containing
Also known as: SKIP
SPHKAP encodes an anchoring protein that binds to and targets protein kinase A type I to specific subcellular compartments, particularly the mitochondrion and muscle Z disc. The gene is highly constrained against loss-of-function variants (pLI=0.94, LOEUF=0.32), but no human disease phenotypes have been reported to date from SPHKAP mutations.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Tolerant to missense variation
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
298 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 25 | 0 | 25 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 239 | 5 | 0 | 244 |
Likely Benign | 0 | 21 | 1 | 3 | 25 |
Benign | 0 | 1 | 1 | 0 | 2 |
| Total | 0 | 261 | 33 | 3 | 297 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SPHKAP · 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
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