Is BDNF p.Asp86= (c.258C>T) pathogenic?

BDNF p.Asp86= (c.258C>T) is classified Likely benign in BDNF (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-12-17). Very rare (popmax 0.00667%, amr); Associated with Inborn genetic diseases.

What condition is associated with BDNF p.Asp86= (c.258C>T)?

BDNF p.Asp86= (c.258C>T) is associated with Inborn genetic diseases (ClinVar).

How common is BDNF p.Asp86= (c.258C>T) in the general population?

BDNF p.Asp86= (c.258C>T) is very rare (popmax 0.00667%, amr) (gnomAD).

BDNF p.Asp86=

c.258C>T · rs78675155 · VCV2759722

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Conditions

Inborn genetic diseases

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 1.8	GERP 0.17, phastCons 1
Overall
CADD	16.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00667% Admixed American · 4/59,994 alleles

Filtering AF 0.00315% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00279%

Overall 0.00347% 56/1,613,976 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	14,999
Remaining individualsnot grpmax-eligible	0.0048%	20,828
European (non-Finnish)	0.00407%	24,584
African / African-American	0.00134%	74,900

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.Asp86=
Coding: c.258C>T
MANE Select: NM_001709
dbSNP: rs78675155
Type: single nucleotide variant
Location: chr11:27658307 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BDNF p.Thr149= Likely benign ★★ same condition
BDNF p.Glu168Ter Likely pathogenic ★ same condition
BDNF p.Ala24Thr Uncertain significance ★ ⚠ same condition
BDNF p.Ala51Val Uncertain significance ★ ⚠ same condition
BDNF p.Arg78Gln Uncertain significance ★ ⚠ same condition
BDNF p.Asp74Ala Uncertain significance ★ ⚠ same condition
BDNF p.Glu111Gln Uncertain significance ★ ⚠ same condition
BDNF p.Gly55Ser 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-asp86 (accessed [today's date]).

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