DIP2A p.Pro149=
c.447C>T · VCV4820806
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0974%, 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 -7.7 | GERP -4.2 |
| Overall | ||
| CADD | 7.939 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0974%
European (non-Finnish) · 1,149/1,179,446 alleles
Filtering AF
0.0927%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0908%
Overall
0.0747%
1,205/1,612,906 alleles · ultra-rare
exomes 1,142/1,460,692 · genomes 63/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0974% | 1,026 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,715 |
| African / African-American | 0.0173% | 5,769 |
| Admixed American | 0.01% | 10,000 |
| East Asian | 0.00892% | 11,214 |
| Finnishnot grpmax-eligible | 0.00787% | 12,707 |
| South Asian | 0.00549% | 18,214 |
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.Pro149=
- Coding
- c.447C>T
- MANE Select
- NM_015151
- Type
- single nucleotide variant
- Location
- chr21:46498625 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.93
- Residue 149
- 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-pro149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown