NIF3L1
Chr 2NGG1 interacting factor 3 like 1
Also known as: ALS2CR1, CALS-7, MDS015
NIF3L1 encodes a protein that functions as a transcriptional corepressor, negatively regulating genes involved in neuronal differentiation through interaction with COPS2. Mutations cause autosomal recessive developmental and epileptic encephalopathy with severe intellectual disability and early-onset seizures. This gene is not highly constrained against loss-of-function mutations.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
ClinVar Variant Classifications
107 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 | 31 | 0 | 31 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 58 | 3 | 0 | 61 |
Likely Benign | 0 | 5 | 0 | 1 | 6 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 63 | 35 | 1 | 99 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NIF3L1 · 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