DNMBP p.Glu20Asp
c.60A>T · VCV4013879
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.8991 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8991 | likely pathogenic |
|---|---|---|
| REVEL | 0.354 | indeterminate |
| SaProt | LLR -7.14 | tolerated |
| ⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -2.5 |
| Regional constraint | o/e 0.75 | unconstrained · MANE · 16 kb · p 1.4e-07 · regional, not allelic |
| Overall | ||
| CADD | 18.23 | 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
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
- DNMBP
- Protein
- p.Glu20Asp
- Coding
- c.60A>T
- MANE Select
- NM_015221
- Type
- single nucleotide variant
- Location
- chr10:99972065 (GRCh38)
- Gene constraint
- LOEUF 0.664 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.91 · 7 PDB
- Residue 20
- the sh3 1 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-glu20asp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown