DIP2B p.Pro669=
c.2007G>A · rs770703708 · VCV722129
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.641%, mid)
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 -10 | GERP -5.2 |
| Overall | ||
| CADD | 1.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.641%
Middle Eastern · 39/6,084 alleles
Filtering AF
0.482%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.427%
Overall
0.0193%
312/1,613,914 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.641% | 156 |
| Remaining individualsnot grpmax-eligible | 0.142% | 702 |
| East Asian | 0.0579% | 1,726 |
| Admixed American | 0.015% | 6,666 |
| European (non-Finnish) | 0.0119% | 8,428 |
| African / African-American | 0.00534% | 18,718 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
| South Asian | 0.00329% | 30,360 |
| Finnishnot grpmax-eligible | 0.00156% | 64,036 |
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
- DIP2B
- Protein
- p.Pro669=
- Coding
- c.2007G>A
- MANE Select
- NM_173602
- dbSNP
- rs770703708
- Type
- single nucleotide variant
- Location
- chr12:50697134 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.83
Similar variants
- DIP2B p.Pro669Leu Uncertain significance ★ ⚠ same residue
- DIP2B p.Asp501Val Uncertain significance ★★ ⚠ same type
- DIP2B p.Cys1071Ser Uncertain significance ★★ ⚠ same type
- DIP2B p.His1027Arg Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile681Val Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile968Thr Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile994Leu Uncertain significance ★★ ⚠ same type
- DIP2B p.Pro244Ala 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/dip2b-p-pro669 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown