Is BDNF p.Arg10Ser (c.28C>A) pathogenic?

BDNF p.Arg10Ser (c.28C>A) is classified Uncertain significance in BDNF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-07). Ultra-rare (popmax 0.0209%, mid); Associated with BDNF-related disorder.

What condition is associated with BDNF p.Arg10Ser (c.28C>A)?

BDNF p.Arg10Ser (c.28C>A) is associated with BDNF-related disorder (ClinVar).

How common is BDNF p.Arg10Ser (c.28C>A) in the general population?

BDNF p.Arg10Ser (c.28C>A) is ultra-rare (popmax 0.0209%, mid) (gnomAD).

BDNF p.Arg10Ser

c.28C>A · VCV3353581

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0209%, mid)

Conditions

BDNF-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 0.15	GERP -4, phastCons 0.005
Overall
CADD	14.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0209% Middle Eastern · 1/4,788 alleles

Filtering AF 0.00153% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000825%

Overall 0.000441% 6/1,361,558 alleles · ultra-rare exomes 3/1,209,378 · genomes 3/152,180 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0209%	4,788
Admixed American	0.00577%	17,317
African / African-American	0.00296%	33,819

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: BDNF
Protein: p.Arg10Ser
Coding: c.28C>A
MANE Select: NM_001709 · reported on NM_001143809
Type: single nucleotide variant
Location: chr11:27701009 (GRCh38)
Gene constraint: LOEUF 0.233 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.44 · 2 PDB

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

Disease context

BDNF-related disorder

Similar variants

BDNF p.Arg10Cys Uncertain significance same residue
BDNF c.-21-15487T>G Uncertain significance ★ same condition
BDNF c.-21-15496C>G Uncertain significance ★ same condition
BDNF p.Arg38Gln Uncertain significance ★ ⚠ same condition
BDNF p.Gly31Asp Uncertain significance ★ ⚠ same condition
BDNF p.Ile10_Ser11insTer Uncertain significance ★ same residue
BDNF p.Lys76Glu Uncertain significance ★ ⚠ same condition
BDNF p.Met220Thr 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/bdnf-p-arg10ser (accessed [today's date]).

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