DIP2A p.Pro333=
c.999G>A · rs201152472 · VCV781523
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.293%, nfe)
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 -20 | GERP -3.8 |
| Overall | ||
| CADD | 0.027 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.293%
European (non-Finnish) · 3,461/1,179,456 alleles
Filtering AF
0.285%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.282%
Overall
0.245%
3,947/1,612,714 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.293% | 341 |
| Remaining individualsnot grpmax-eligible | 0.215% | 466 |
| Admixed American | 0.159% | 629 |
| South Asian | 0.158% | 631 |
| African / African-American | 0.0734% | 1,362 |
| Finnishnot grpmax-eligible | 0.0641% | 1,561 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0542% | 1,845 |
| East Asian | 0.00223% | 44,792 |
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
- DIP2A
- Protein
- p.Pro333=
- Coding
- c.999G>A
- MANE Select
- NM_015151
- dbSNP
- rs201152472
- Type
- single nucleotide variant
- Location
- chr21:46511511 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.93
Similar variants
- DIP2A p.Pro333Leu Uncertain significance ★ ⚠ same residue
- DIP2A p.Ala676Thr Uncertain significance ★★ ⚠ same type
- DIP2A p.Glu832Lys Uncertain significance ★★ ⚠ 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-pro333 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown