Is BNC2 p.Arg232= (c.696C>G) pathogenic?

BNC2 p.Arg232= (c.696C>G) is classified Uncertain significance in BNC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-23). Absent from gnomAD v4.1; Associated with BNC2-related disorder.

What condition is associated with BNC2 p.Arg232= (c.696C>G)?

BNC2 p.Arg232= (c.696C>G) is associated with BNC2-related disorder (ClinVar).

How common is BNC2 p.Arg232= (c.696C>G) in the general population?

BNC2 p.Arg232= (c.696C>G) is absent from gnomAD v4.1 (gnomAD).

BNC2 p.Arg232=

c.696C>G · rs2547719780 · VCV2629180

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

BNC2-related disorder

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 6.8	GERP 0.94, phastCons 1
Overall
CADD	9.134	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BNC2
Protein: p.Arg232=
Coding: c.696C>G
MANE Select: NM_017637
dbSNP: rs2547719780
Type: single nucleotide variant
Location: chr9:16437498 (GRCh38)
Gene constraint: LOEUF 0.365 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.10

Full BNC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BNC2-related disorder

Similar variants

BNC2 p.Arg232Cys Uncertain significance ★ ⚠ same residue
BNC2 c.129+6T>G Uncertain significance same condition
BNC2 c.669+10G>A Likely benign same condition
BNC2 p.Ala954Thr Benign/Likely benign same condition
BNC2 p.Ala386Val Uncertain significance ★★ ⚠ same type
BNC2 p.Arg536Gln Uncertain significance ★★ ⚠ same type
BNC2 p.Arg875His Uncertain significance ★★ ⚠ same type
BNC2 p.Asn1032Ser Uncertain significance ★★ ⚠ same type

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/bnc2-p-arg232 (accessed [today's date]).

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