Is DNMT3A p.Gly869Ala (c.2606G>C) pathogenic?

DNMT3A p.Gly869Ala (c.2606G>C) is classified Likely pathogenic in DNMT3A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-18). AlphaMissense: likely pathogenic (0.9962); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DNMT3A p.Gly869Ala (c.2606G>C)?

DNMT3A p.Gly869Ala (c.2606G>C) is associated with Inborn genetic diseases (ClinVar).

How common is DNMT3A p.Gly869Ala (c.2606G>C) in the general population?

DNMT3A p.Gly869Ala (c.2606G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNMT3A p.Gly869Ala (c.2606G>C)?

AlphaMissense predicts likely pathogenic (score 0.9962) — an in-silico prediction, not a clinical call.

DNMT3A p.Gly869Ala

c.2606G>C · VCV3273244

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9962 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,028)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9962	likely pathogenic ✓ concordant with ClinVar
REVEL	0.975	strongly pathogenic-leaning
SaProt	LLR -13.92	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.45	unconstrained · MANE · 2,612 bp · p 2.9e-07 · regional, not allelic
Overall
CADD	29.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,028). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DNMT3A
Protein: p.Gly869Ala
Coding: c.2606G>C
MANE Select: NM_022552
Type: single nucleotide variant
Location: chr2:25234412 (GRCh38)
Gene constraint: LOEUF 1.998 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 73.97 · 47 PDB
Residue 869: the sam-dependent mtase c5-type domain

Full DNMT3A 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

DNMT3A p.Arg301Trp Pathogenic/Likely pathogenic ★★ same condition
DNMT3A p.Arg320Ter Pathogenic/Likely pathogenic ★★ same condition
DNMT3A p.Arg688His Pathogenic/Likely pathogenic ★★ same condition
DNMT3A p.Met548Thr Pathogenic/Likely pathogenic ★★ same condition
DNMT3A p.Pro904Leu Pathogenic/Likely pathogenic ★★ same condition
DNMT3A c.448+48C>G Uncertain significance ★★ same condition
DNMT3A p.Arg544His Uncertain significance ★★ ⚠ same condition
DNMT3A p.Arg596Gln 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/dnmt3a-p-gly869ala (accessed [today's date]).

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