Is DNMT3B p.Val424Ile (c.1270G>A) pathogenic?

DNMT3B p.Val424Ile (c.1270G>A) is classified Uncertain significance in DNMT3B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-13). AlphaMissense: likely benign (0.0779); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DNMT3B p.Val424Ile (c.1270G>A)?

DNMT3B p.Val424Ile (c.1270G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DNMT3B p.Val424Ile (c.1270G>A) in the general population?

DNMT3B p.Val424Ile (c.1270G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNMT3B p.Val424Ile (c.1270G>A)?

AlphaMissense predicts likely benign (score 0.0779) — an in-silico prediction, not a clinical call.

DNMT3B p.Val424Ile

c.1270G>A · VCV3273247

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0779 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0779	likely benign
REVEL	0.341	indeterminate
SaProt	LLR -6.78	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP -0.31, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 5,534 bp · p 0.3 · regional, not allelic
Overall
CADD	21.7	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

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: DNMT3B
Protein: p.Val424Ile
Coding: c.1270G>A
MANE Select: NM_006892
Type: single nucleotide variant
Location: chr20:32795667 (GRCh38)
Gene constraint: LOEUF 0.396 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.18 · 47 PDB
Residue 424: the add domain; an α-helix

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.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
DNMT3B p.Asn786Lys 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-val424ile (accessed [today's date]).

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