PITPNM3
Chr 17ADPITPNM family member 3
Also known as: ACKR6, CORD5, NIR1, RDGBA3
This protein catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes and binds calcium ions. Mutations cause autosomal dominant cone-rod dystrophy 5, affecting retinal function and vision. The gene is highly constrained against loss-of-function variants (pLI 1.0, LOEUF 0.21), indicating intolerance to protein-disrupting mutations.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Moderately missense-constrained (top ~2.5%)
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
500 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 | 1 | 0 | 10 | 0 | 11 |
Likely Pathogenic | 1 | 0 | 0 | 0 | 1 |
VUS | 5 | 220 | 50 | 1 | 276 |
Likely Benign | 0 | 3 | 63 | 92 | 158 |
Benign | 0 | 2 | 37 | 4 | 43 |
Conflicting | — | 11 | |||
| Total | 7 | 225 | 160 | 97 | 500 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PITPNM3 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
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