SLC31A1
Chr 9ARsolute carrier family 31 member 1
Also known as: COPT1, CTR1, NSCT
The protein is a high-affinity copper transporter that mediates copper uptake from the extracellular space to the cytoplasm and delivers copper directly to specific chaperones to control intracellular copper levels. Autosomal recessive mutations cause neurodegeneration and seizures due to copper transport defect. The pathogenic mechanism appears to involve dominant-negative effects that disrupt normal copper homeostasis.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
61 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 | 1 | 25 | 0 | 26 |
Likely Pathogenic | 0 | 1 | 3 | 0 | 4 |
VUS | 0 | 18 | 3 | 0 | 21 |
Likely Benign | 0 | 2 | 1 | 0 | 3 |
Benign | 0 | 1 | 0 | 1 | 2 |
| Total | 0 | 23 | 32 | 1 | 56 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SLC31A1 · 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