Is BSN p.Arg110Ter (c.328C>T) pathogenic?

BSN p.Arg110Ter (c.328C>T) is classified Uncertain significance in BSN (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-16). Very rare (popmax 0.000255%, nfe); Associated with BSN related epilepsy.

What condition is associated with BSN p.Arg110Ter (c.328C>T)?

BSN p.Arg110Ter (c.328C>T) is associated with BSN related epilepsy (ClinVar).

How common is BSN p.Arg110Ter (c.328C>T) in the general population?

BSN p.Arg110Ter (c.328C>T) is very rare (popmax 0.000255%, nfe) (gnomAD).

BSN p.Arg110Ter

c.328C>T · rs757868271 · VCV2582612

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000255%, nfe)

Conditions

BSN related epilepsy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 2 of 12
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP 0.71, phastCons 0.46
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000255% European (non-Finnish) · 3/1,177,320 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000206% 3/1,455,526 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: BSN
Protein: p.Arg110Ter
Coding: c.328C>T
MANE Select: NM_003458
dbSNP: rs757868271
Type: single nucleotide variant
Location: chr3:49625078 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 (gnomAD)
Residue 110: the 'disordered' region

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

Disease context

BSN related epilepsy

Similar variants

BSN p.Arg1145Trp Uncertain significance ★★ ⚠ same condition
BSN p.Leu2466Ile Uncertain significance ★★ ⚠ same condition
BSN p.Pro2732Arg Uncertain significance ★★ same condition
BSN p.Gln1776Ter Likely pathogenic ★ same condition
BSN p.Gln3155Ter Likely pathogenic ★ same condition
BSN p.Gln875Ter Pathogenic ★ same condition
BSN p.Arg1066Cys Uncertain significance ★ ⚠ same condition
BSN p.Arg1335Ter Conflicting classifications of pathogenicity ★ ⚠ 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/bsn-p-arg110ter (accessed [today's date]).

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