NBN p.Asp201del
c.600TGA[1] · rs755050499 · VCV627767
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
4
acute lymphoblastic leukemia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -1, phastCons 0.68 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,280 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,460,548 alleles · very rare
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
- NBN
- Protein
- p.Asp201del
- Coding
- c.600TGA[1]
- MANE Select
- NM_057091 · reported on NM_002485
- dbSNP
- rs755050499
- Type
- Microsatellite
- Location
- chr8:89971270 (GRCh38)
- Structure
- AlphaFold pLDDT 75.83 · 5 PDB
- Residue 201
- a disulfide bond
Similar variants
- NBN p.Asp201Asn Uncertain significance ★★ ⚠ same residue
- NBN p.Asp201Gly Uncertain significance ★★ ⚠ same residue
- NBN p.Asp201His Uncertain significance ★★ same residue
- NBN p.Asp201Val Uncertain significance ★★ ⚠ same residue
- NBN p.Asp201Glu Uncertain significance ★ ⚠ same residue
- NBN p.Ala32fs Pathogenic/Likely pathogenic ★★ same condition
- NBN p.Gln494fs Pathogenic ★★ same condition
- NBN p.Ser347fs Pathogenic ★★ same condition
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/nbn-p-asp201del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown