NBN p.Leu165=
c.495C>A · rs764290829 · VCV1744377
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,586,994)
Conditions
2
Nijmegen breakage syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 6.574 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,586,994). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- NBN
- Protein
- p.Leu165=
- Coding
- c.495C>A
- MANE Select
- NM_057091 · reported on NM_002485
- dbSNP
- rs764290829
- Type
- single nucleotide variant
- Location
- chr8:89978309 (GRCh38)
- Structure
- AlphaFold pLDDT 75.83 · 5 PDB
- Residue 165
- a disulfide bond; an α-helix
Similar variants
- NBN p.Leu165Ile Uncertain significance ★★ ⚠ same residue
- NBN p.Leu165Arg Uncertain significance ★ ⚠ same residue
- NBN p.Leu165Phe Uncertain significance ★ ⚠ same residue
- NBN p.Leu165fs Pathogenic ★★ same residue
- NBN c.1124+1G>C Likely pathogenic ★★ same condition
- NBN c.1124+2T>G Likely pathogenic ★★ same condition
- NBN c.1397+2T>A Likely pathogenic ★★ same condition
- NBN c.171+1G>A Likely 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-leu165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown