DIP2C p.Pro52=
c.156G>A · rs753310455 · VCV2077020
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.34 | donor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.65 | GERP -3.7, phastCons 0.021 |
| Overall | ||
| CADD | 8.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
Admixed American · 9/57,622 alleles
Filtering AF
0.00812%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.006%
Overall
0.000876%
14/1,598,098 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0156% | 6,402 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,754 |
| African / African-American | 0.00135% | 74,164 |
| European (non-Finnish) | 0.000256% | 390,877 |
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.Pro52=
- Coding
- c.156G>A
- MANE Select
- NM_014974
- dbSNP
- rs753310455
- Type
- single nucleotide variant
- Location
- chr10:486460 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.64
- Residue 52
- the dmap1-binding domain; the 'disordered' region
Similar variants
- DIP2C p.Pro52Leu 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-pro52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown