NBAS p.Asp398fs
c.1194_1195del · VCV3544478
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Leber congenital amaurosis
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 -0.016 | GERP -3.8 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NBAS
- Protein
- p.Asp398fs
- Coding
- c.1194_1195del
- MANE Select
- NM_015909
- Type
- Deletion
- Location
- chr2:15475833 (GRCh38)
- Gene constraint
- LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.42
- Residue 398
- a UniProt-annotated variant site (in ilfs2; uncertain significance); the 'interaction with use1' region
Disease context
Leber congenital amaurosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Leber congenital amaurosis (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- NBAS p.Asp398Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- NBAS p.Asp398= Likely benign ★ same residue
- NBAS p.Asp1891Asn Uncertain significance ★ ⚠ same condition
- 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
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-asp398fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown