Is BSN p.Ser3769= (c.11307T>C) pathogenic?

BSN p.Ser3769= (c.11307T>C) is classified Likely benign in BSN (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-18). Ultra-rare (popmax 0.0156%, eas); Associated with BSN-related disorder.

What condition is associated with BSN p.Ser3769= (c.11307T>C)?

BSN p.Ser3769= (c.11307T>C) is associated with BSN-related disorder (ClinVar).

How common is BSN p.Ser3769= (c.11307T>C) in the general population?

BSN p.Ser3769= (c.11307T>C) is ultra-rare (popmax 0.0156%, eas) (gnomAD).

BSN p.Ser3769=

c.11307T>C · rs763460708 · VCV3033876

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0156%, eas)

Conditions

BSN-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 -5	GERP -4.4
Overall
CADD	0.172	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0156% East Asian · 7/44,890 alleles

Filtering AF 0.00726% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.00105% 17/1,612,604 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0156%	6,413
Remaining individualsnot grpmax-eligible	0.0112%	8,920
South Asian	0.00329%	30,362

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.Ser3769=
Coding: c.11307T>C
MANE Select: NM_003458
dbSNP: rs763460708
Type: single nucleotide variant
Location: chr3:49663465 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 (gnomAD)
Residue 3769: the 'disordered' region

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

Disease context

BSN-related disorder

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.Arg110Ter Uncertain significance ★ 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-ser3769 (accessed [today's date]).

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