Is DNMT3B p.Ala26Pro (c.76G>C) pathogenic?

DNMT3B p.Ala26Pro (c.76G>C) is classified Uncertain significance in DNMT3B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). AlphaMissense: likely benign (0.088); Very rare (popmax 0.00167%, amr); Associated with Inborn genetic diseases.

What condition is associated with DNMT3B p.Ala26Pro (c.76G>C)?

DNMT3B p.Ala26Pro (c.76G>C) is associated with Inborn genetic diseases (ClinVar).

How common is DNMT3B p.Ala26Pro (c.76G>C) in the general population?

DNMT3B p.Ala26Pro (c.76G>C) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about DNMT3B p.Ala26Pro (c.76G>C)?

AlphaMissense predicts likely benign (score 0.088) — an in-silico prediction, not a clinical call.

DNMT3B p.Ala26Pro

c.76G>C · VCV4243639

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.088 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.088	likely benign
REVEL	0.207	benign-leaning
SaProt	LLR -7.67	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.6	GERP 0.81, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 8,530 bp · p 0.27 · regional, not allelic
Overall
CADD	15.83	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00167% Admixed American · 1/60,020 alleles

Overall 0.000124% 2/1,613,878 alleles · very rare exomes 2/1,461,706 · genomes 0/152,172 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,020
European (non-Finnish)	8.47e-05%	1,179,988

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: DNMT3B
Protein: p.Ala26Pro
Coding: c.76G>C
MANE Select: NM_006892
Type: single nucleotide variant
Location: chr20:32780399 (GRCh38)
Gene constraint: LOEUF 0.396 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.18 · 47 PDB
Residue 26: the 'interaction with dnmt1 and dnmt3a' region; the 'disordered' region

Full DNMT3B 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

DNMT3B p.Ala26= Likely benign ★ same residue
DNMT3B p.Ala569Thr Uncertain significance ★★ ⚠ same condition
DNMT3B p.Arg122His Uncertain significance ★★ ⚠ same condition
DNMT3B p.Arg148Trp Uncertain significance ★★ ⚠ same condition
DNMT3B p.Arg149Gln Uncertain significance ★★ ⚠ same condition
DNMT3B p.Arg190Cys Uncertain significance ★★ ⚠ same condition
DNMT3B p.Arg459Gln Uncertain significance ★★ ⚠ same condition
DNMT3B p.Arg97His 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/dnmt3b-p-ala26pro (accessed [today's date]).

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