DNMBP p.Glu861=
c.2583G>A · rs12260203 · VCV3038596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.013 | GERP -2, phastCons 0.86 |
| Overall | ||
| CADD | 5.895 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
African / African-American · 967/75,046 alleles
Filtering AF
1.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.19%
Overall
0.0856%
1,382/1,614,150 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.29% | 78 |
| Admixed American | 0.157% | 638 |
| Ashkenazi Jewishnot grpmax-eligible | 0.118% | 846 |
| Remaining individualsnot grpmax-eligible | 0.106% | 947 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.0185% | 5,413 |
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
- DNMBP
- Protein
- p.Glu861=
- Coding
- c.2583G>A
- MANE Select
- NM_015221
- dbSNP
- rs12260203
- Type
- single nucleotide variant
- Location
- chr10:99900038 (GRCh38)
- Gene constraint
- LOEUF 0.664 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.91 · 7 PDB
- Residue 861
- a UniProt-annotated variant site (in ctrct48); the dh domain
Similar variants
- DNMBP p.Arg1326His Uncertain significance ★★ ⚠ same type
- DNMBP p.Asn1560Lys Uncertain significance ★★ ⚠ same type
- DNMBP p.Ser984Cys Uncertain significance ★★ ⚠ same type
- DNMBP c.2554+8C>T Benign/Likely benign ★★ same type
- DNMBP c.3156+7A>G Benign ★★ same type
- DNMBP p.Asn373Lys Benign ★★ same type
- DNMBP p.Asn961= Benign ★★ same type
- DNMBP p.Cys1413Trp Benign ★★ same type
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/dnmbp-p-glu861 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown