Is DNMT3A p.Tyr735Cys (c.2204A>G) pathogenic?

DNMT3A p.Tyr735Cys (c.2204A>G) is classified Conflicting classifications of pathogenicity in DNMT3A (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-01-13). AlphaMissense: likely pathogenic (0.9459); Very rare (popmax 0.00502%, amr); Associated with Tatton-Brown-Rahman overgrowth syndrome.

What condition is associated with DNMT3A p.Tyr735Cys (c.2204A>G)?

DNMT3A p.Tyr735Cys (c.2204A>G) is associated with Tatton-Brown-Rahman overgrowth syndrome, diffuse large B-cell lymphoma (ClinVar).

How common is DNMT3A p.Tyr735Cys (c.2204A>G) in the general population?

DNMT3A p.Tyr735Cys (c.2204A>G) is very rare (popmax 0.00502%, amr) (gnomAD).

What do computational predictors say about DNMT3A p.Tyr735Cys (c.2204A>G)?

AlphaMissense predicts likely pathogenic (score 0.9459) — an in-silico prediction, not a clinical call.

DNMT3A p.Tyr735Cys

c.2204A>G · rs147828672 · VCV812892

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely pathogenic

0.9459 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00502%, amr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Tatton-Brown-Rahman overgrowth syndrome

Computational evidence

Protein change
AlphaMissense	0.9459	likely pathogenic
REVEL	0.895	moderately pathogenic-leaning
SaProt	LLR -13.51	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 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 1.40	unconstrained · MANE · 4,806 bp · p 8.9e-10 · regional, not allelic
Overall
CADD	32.0	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

Grpmax group 0.00502% Admixed American · 3/59,756 alleles

Filtering AF 0.00188% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00164%

Overall 0.00292% 47/1,611,786 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0204%	4,907
Admixed Americangrpmax	0.00502%	19,919
African / African-American	0.00402%	24,901
European (non-Finnish)	0.00263%	38,031
East Asian	0.00223%	44,864
Remaining individualsnot grpmax-eligible	0.0016%	62,404
Finnishnot grpmax-eligible	0.00157%	63,876
South Asian	0.0011%	90,804

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.Tyr735Cys
Coding: c.2204A>G
MANE Select: NM_022552
dbSNP: rs147828672
Type: single nucleotide variant
Location: chr2:25240420 (GRCh38)
Gene constraint: LOEUF 1.998 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 73.97 · 47 PDB
Residue 735: 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

Tatton-Brown-Rahman overgrowth syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: diffuse large B-cell lymphoma

Similar variants

DNMT3A p.Tyr735Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
DNMT3A p.Tyr735His 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-tyr735cys (accessed [today's date]).

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