Is NBN p.Ser88= (c.264C>T) pathogenic?

NBN p.Ser88= (c.264C>T) is classified Likely benign in NBN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-05-06). Absent from gnomAD v4.1; Associated with Nijmegen breakage syndrome.

What condition is associated with NBN p.Ser88= (c.264C>T)?

NBN p.Ser88= (c.264C>T) is associated with Nijmegen breakage syndrome, hereditary neoplastic syndrome (ClinVar).

How common is NBN p.Ser88= (c.264C>T) in the general population?

NBN p.Ser88= (c.264C>T) is absent from gnomAD v4.1 (gnomAD).

NBN p.Ser88=

c.264C>T · rs2129914967 · VCV1657319

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 1,613,858)

Conditions

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 -0.041	GERP -3.8, phastCons 0.001
Overall
CADD	1.508	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,858). 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.Ser88=
Coding: c.264C>T
MANE Select: NM_057091 · reported on NM_002485
dbSNP: rs2129914967
Type: single nucleotide variant
Location: chr8:89981431 (GRCh38)
Structure: AlphaFold pLDDT 75.83 · 5 PDB
Residue 88: the 'disordered' region

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

Disease context

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

Also linked: hereditary neoplastic syndrome

Similar variants

NBN p.Ser88Phe Uncertain significance ★★ ⚠ same residue
NBN p.Ser88fs 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
NBN c.172-2A>G 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-ser88 (accessed [today's date]).

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