DIP2C p.Pro1060=
c.3180G>A · rs146207311 · VCV1603559
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.616%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.46 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -3.7 |
| Overall | ||
| CADD | 4.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.616%
African / African-American · 462/75,010 alleles
Filtering AF
0.569%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.551%
Overall
0.0314%
506/1,613,814 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.616% | 162 |
| Admixed American | 0.0233% | 4,283 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,208 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00136% | 73,747 |
| South Asian | 0.0011% | 91,024 |
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
- DIP2C
- Protein
- p.Pro1060=
- Coding
- c.3180G>A
- MANE Select
- NM_014974
- dbSNP
- rs146207311
- Type
- single nucleotide variant
- Location
- chr10:348692 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.64
Similar variants
- DIP2C p.Pro1060Leu Uncertain significance ★ ⚠ same residue
- DIP2C p.Ala1066Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1066Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1101Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1155Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1466Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala193Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala422Thr 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/dip2c-p-pro1060 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown