Is DNMT3A p.Arg379Cys (c.1135C>T) pathogenic?

DNMT3A p.Arg379Cys (c.1135C>T) is classified Uncertain significance in DNMT3A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-04-21). AlphaMissense: likely pathogenic (0.9948); Very rare (popmax 0.00333%, amr); Associated with DNMT3A-related disorder.

What condition is associated with DNMT3A p.Arg379Cys (c.1135C>T)?

DNMT3A p.Arg379Cys (c.1135C>T) is associated with DNMT3A-related disorder, Tatton-Brown-Rahman overgrowth syndrome (ClinVar).

How common is DNMT3A p.Arg379Cys (c.1135C>T) in the general population?

DNMT3A p.Arg379Cys (c.1135C>T) is very rare (popmax 0.00333%, amr) (gnomAD).

What do computational predictors say about DNMT3A p.Arg379Cys (c.1135C>T)?

AlphaMissense predicts likely pathogenic (score 0.9948) — an in-silico prediction, not a clinical call.

DNMT3A p.Arg379Cys

c.1135C>T · rs754459010 · VCV434957

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.9948 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DNMT3A-related disorder

Computational evidence

Protein change
AlphaMissense	0.9948	likely pathogenic
REVEL	0.655	pathogenic-leaning
SaProt	LLR -15.81	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 9.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 3,445 bp · p 4.3e-09 · regional, not allelic
Overall
CADD	27.3	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

Grpmax group 0.00333% Admixed American · 2/60,018 alleles

Filtering AF 0.000553% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000207%

Overall 0.000682% 11/1,613,456 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,596
Admixed Americangrpmax	0.00333%	30,009
African / African-American	0.00133%	75,058
European (non-Finnish)	0.000593%	168,563

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DNMT3A
Protein: p.Arg379Cys
Coding: c.1135C>T
MANE Select: NM_022552
dbSNP: rs754459010
Type: single nucleotide variant
Location: chr2:25246764 (GRCh38)
Gene constraint: LOEUF 1.998 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 73.97 · 47 PDB
Residue 379: the 'interaction with dnmt1 and dnmt3b' region; an α-helix

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

Disease context

DNMT3A-related disorder

Also linked: Tatton-Brown-Rahman overgrowth syndrome

Similar variants

DNMT3A p.Arg379= Likely benign ★★ same residue
DNMT3A p.Arg379His Uncertain significance ★ ⚠ same residue
DNMT3A c.1667+1G>A Likely pathogenic ★★ same condition
DNMT3A c.1937-2A>G Pathogenic ★★ same condition
DNMT3A c.2478+1G>A Pathogenic/Likely pathogenic ★★ same condition
DNMT3A c.2479-1G>A Likely pathogenic ★★ same condition
DNMT3A p.Arg143Ter Pathogenic ★★ same condition
DNMT3A p.Arg320Ter Pathogenic/Likely pathogenic ★★ 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-arg379cys (accessed [today's date]).

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