Is NBN p.Val25= (c.75T>G) pathogenic?

NBN p.Val25= (c.75T>G) is classified Likely benign in NBN (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-10-13). Very rare (popmax 0.00017%, nfe); Associated with acute lymphoblastic leukemia.

What condition is associated with NBN p.Val25= (c.75T>G)?

NBN p.Val25= (c.75T>G) is associated with acute lymphoblastic leukemia, Nijmegen breakage syndrome, hereditary neoplastic syndrome (ClinVar).

How common is NBN p.Val25= (c.75T>G) in the general population?

NBN p.Val25= (c.75T>G) is very rare (popmax 0.00017%, nfe) (gnomAD).

NBN p.Val25=

c.75T>G · rs1000181272 · VCV481841

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Conditions

acute lymphoblastic leukemia

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 0.67	GERP -5, phastCons 0.94
Overall
CADD	7.263	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00017% European (non-Finnish) · 2/1,179,662 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,613,580 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.Val25=
Coding: c.75T>G
MANE Select: NM_057091 · reported on NM_002485
dbSNP: rs1000181272
Type: single nucleotide variant
Location: chr8:89982818 (GRCh38)
Structure: AlphaFold pLDDT 75.83 · 5 PDB

Full NBN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

acute lymphoblastic leukemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Nijmegen breakage syndrome hereditary neoplastic syndrome aplastic anemia

Similar variants

NBN p.Val25Phe Uncertain significance ★★ ⚠ same residue
NBN p.Val25Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
NBN p.Val25fs Likely 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
NBN c.172-1G>T 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-val25 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown