DNMT3B p.Arg832=
c.2496G>A · rs1209737690 · VCV2789149
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Conditions
1
immunodeficiency-centromeric instability-facial anomalies syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.326 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.4 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 11.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,032 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000205%
3/1,461,892 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,016 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
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.Arg832=
- Coding
- c.2496G>A
- MANE Select
- NM_006892
- dbSNP
- rs1209737690
- Type
- single nucleotide variant
- Location
- chr20:32807837 (GRCh38)
- Gene constraint
- LOEUF 0.396 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.18 · 47 PDB
- Residue 832
- a binding site; the sam-dependent mtase c5-type domain
Similar variants
- DNMT3B c.2421-11G>A Pathogenic/Likely pathogenic ★★ same condition
- DNMT3B p.Ala603Thr Pathogenic/Likely pathogenic ★★ same condition
- DNMT3B p.Arg826Cys Pathogenic/Likely pathogenic ★★ same condition
- DNMT3B p.Arg840Gln Likely pathogenic ★★ same condition
- DNMT3B p.Asp653Asn Pathogenic/Likely pathogenic ★★ same condition
- DNMT3B p.His814Arg Likely pathogenic ★★ ⚠ same condition
- DNMT3B p.Val613Ala Pathogenic/Likely pathogenic ★★ same condition
- DNMT3B p.Val726Gly 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/dnmt3b-p-arg832 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown