Is NBN p.His45= (c.135T>C) pathogenic?

NBN p.His45= (c.135T>C) is classified Likely benign in NBN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-17). Very rare (popmax 0.00223%, eas); Associated with hereditary neoplastic syndrome.

What condition is associated with NBN p.His45= (c.135T>C)?

NBN p.His45= (c.135T>C) is associated with hereditary neoplastic syndrome, Nijmegen breakage syndrome (ClinVar).

How common is NBN p.His45= (c.135T>C) in the general population?

NBN p.His45= (c.135T>C) is very rare (popmax 0.00223%, eas) (gnomAD).

NBN p.His45=

c.135T>C · rs770618624 · VCV492089

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

hereditary neoplastic 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 0.86	GERP -3.3, phastCons 0.98
Overall
CADD	8.501	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,848 alleles

Overall 0.000137% 2/1,461,716 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,848
European (non-Finnish)	8.47e-05%	1,179,944

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.His45=
Coding: c.135T>C
MANE Select: NM_057091 · reported on NM_002485
dbSNP: rs770618624
Type: single nucleotide variant
Location: chr8:89982758 (GRCh38)
Structure: AlphaFold pLDDT 75.83 · 5 PDB
Residue 45: the 'disordered' region

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Nijmegen breakage syndrome

Similar variants

NBN p.His45Asp Uncertain significance ★★ ⚠ same residue
NBN p.His45Gln Uncertain significance ★★ ⚠ same residue
NBN p.His45Tyr Uncertain significance ★★ ⚠ same residue
NBN p.His45Arg Uncertain significance ★ ⚠ 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-his45 (accessed [today's date]).

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