DIP2A p.Glu110Lys
c.328G>A · VCV4660114
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.6212 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.6212 | likely pathogenic |
|---|---|---|
| REVEL | 0.287 | benign-leaning |
| SaProt | LLR -7.31 | tolerated |
| ⇒ AlphaMissense calls this damaging; REVEL and SaProt do not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 0.85 | unconstrained · MANE · 108 kb · p 1.5e-11 · regional, not allelic |
| Overall | ||
| CADD | 29.0 | 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
- DIP2A
- Protein
- p.Glu110Lys
- Coding
- c.328G>A
- MANE Select
- NM_015151
- Type
- single nucleotide variant
- Location
- chr21:46497032 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.93
- Residue 110
- the dmap1-binding domain; the 'disordered' region
Similar variants
- DIP2A p.Ala676Thr Uncertain significance ★★ ⚠ same type
- DIP2A p.Glu832Lys Uncertain significance ★★ ⚠ same type
- DIP2A p.Pro333= Benign ★★ same type
- DIP2A p.Pro798Leu Benign/Likely benign ★★ ⚠ same type
- DIP2A p.Thr848= Benign/Likely benign ★★ same type
- DIP2A p.Val1531= Benign ★★ same type
- DIP2A c.1429+2T>G Likely pathogenic ★ same type
- DIP2A c.2395-2A>G Uncertain significance ★ 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/dip2a-p-glu110lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown