NBAS p.Thr402fs
c.1203del · rs1572903776 · VCV817987
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 14 of 52 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 0.85, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NBAS
- Protein
- p.Thr402fs
- Coding
- c.1203del
- MANE Select
- NM_015909
- dbSNP
- rs1572903776
- Type
- Deletion
- Location
- chr2:15475825 (GRCh38)
- Gene constraint
- LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.42
- Residue 402
- a UniProt-annotated variant site (in ilfs2; uncertain significance); the 'interaction with use1' region
Similar variants
- NBAS p.Asp2149_Ile2150insTer Pathogenic/Likely pathogenic ★★ same type
- NBAS p.Cys1112fs Pathogenic ★★ same type
- NBAS p.Gln2232fs Pathogenic/Likely pathogenic ★★ same type
- NBAS p.Gln44fs Pathogenic/Likely pathogenic ★★ same type
- NBAS p.Glu1092fs Pathogenic/Likely pathogenic ★★ same type
- NBAS p.Ile984fs Pathogenic/Likely pathogenic ★★ same type
- NBAS p.Leu1507fs Pathogenic/Likely pathogenic ★★ same type
- NBAS p.Leu1726fs Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nbas-p-thr402fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown