DDI1 p.Pro41=
c.123C>T · rs138352725 · VCV770220
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.49%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.026 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.35 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.8 |
| Overall | ||
| CADD | 0.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.49%
Admixed American · 1,496/60,030 alleles
Filtering AF
2.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.34%
Overall
0.143%
2,309/1,614,198 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.49% | 40 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| African / African-American | 0.0573% | 1,746 |
| European (non-Finnish) | 0.0556% | 1,799 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.0165% | 6,072 |
| Finnishnot grpmax-eligible | 0.0125% | 8,004 |
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
- DDI1
- Protein
- p.Pro41=
- Coding
- c.123C>T
- MANE Select
- NM_001001711
- dbSNP
- rs138352725
- Type
- single nucleotide variant
- Location
- chr11:104036945 (GRCh38)
- Gene constraint
- LOEUF 1.337 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.27 · 1 PDB
- Residue 41
- the ubiquitin-like domain
Similar variants
- DDI1 p.Asp323Asn Benign ★★ same type
- DDI1 p.His155= Benign ★★ same type
- DDI1 p.Thr178= Benign ★★ same type
- DDI1 p.Ala100Val Uncertain significance ★ ⚠ same type
- DDI1 p.Ala36Gly Uncertain significance ★ ⚠ same type
- DDI1 p.Ala84Val Uncertain significance ★ ⚠ same type
- DDI1 p.Arg108Gly Uncertain significance ★ ⚠ same type
- DDI1 p.Arg124Pro 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/ddi1-p-pro41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown