Is DNMT3A p.Ser839Phe (c.2516C>T) pathogenic?

DNMT3A p.Ser839Phe (c.2516C>T) is classified Uncertain significance in DNMT3A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-21). AlphaMissense: likely pathogenic (0.9995); Absent from gnomAD v4.1; Associated with DNMT3A-related disorder.

What condition is associated with DNMT3A p.Ser839Phe (c.2516C>T)?

DNMT3A p.Ser839Phe (c.2516C>T) is associated with DNMT3A-related disorder (ClinVar).

How common is DNMT3A p.Ser839Phe (c.2516C>T) in the general population?

DNMT3A p.Ser839Phe (c.2516C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNMT3A p.Ser839Phe (c.2516C>T)?

AlphaMissense predicts likely pathogenic (score 0.9995) — an in-silico prediction, not a clinical call.

DNMT3A p.Ser839Phe

c.2516C>T · rs2465329881 · VCV2630862

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9995 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DNMT3A-related disorder

Computational evidence

Protein change
AlphaMissense	0.9995	likely pathogenic · top 7% in DNMT3A
REVEL	0.901	moderately pathogenic-leaning
SaProt	LLR -14.47	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 10	GERP 1.7, phastCons 1
Regional constraint	o/e 0.45	unconstrained · MANE · 2,612 bp · p 2.9e-07 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

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: DNMT3A
Protein: p.Ser839Phe
Coding: c.2516C>T
MANE Select: NM_022552
dbSNP: rs2465329881
Type: single nucleotide variant
Location: chr2:25235788 (GRCh38)
Gene constraint: LOEUF 1.998 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 73.97 · 47 PDB
Residue 839: an α-helix; the sam-dependent mtase c5-type domain

Full DNMT3A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNMT3A-related disorder

Similar variants

DNMT3A c.1667+1G>A Likely pathogenic ★★ same condition
DNMT3A p.Arg771Ter Pathogenic/Likely pathogenic ★★ same condition
DNMT3A p.Leu508Pro Pathogenic/Likely pathogenic ★★ same condition
DNMT3A p.Trp601Ter Pathogenic ★★ same condition
DNMT3A p.Val636Met Likely pathogenic ★★ same condition
DNMT3A p.Arg379Cys Uncertain significance ★★ ⚠ same condition
DNMT3A p.Arg55His Uncertain significance ★★ ⚠ same condition
DNMT3A p.Ile490Thr 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-ser839phe (accessed [today's date]).

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