DCPS p.Ile302=
c.906C>T · rs148207687 · VCV733666
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.111%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.29 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.23 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP 0.59 |
| Overall | ||
| CADD | 7.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
East Asian · 50/44,882 alleles
Filtering AF
0.0963%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0943%
Overall
0.0837%
1,351/1,614,096 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.111% | 898 |
| European (non-Finnish) | 0.101% | 989 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Middle Eastern | 0.0495% | 2,021 |
| African / African-American | 0.0267% | 3,752 |
| Admixed American | 0.0233% | 4,287 |
| Finnishnot grpmax-eligible | 0.0219% | 4,567 |
| South Asian | 0.00988% | 10,121 |
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
- DCPS
- Protein
- p.Ile302=
- Coding
- c.906C>T
- MANE Select
- NM_014026
- dbSNP
- rs148207687
- Type
- single nucleotide variant
- Location
- chr11:126345505 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.18 · 11 PDB
- Residue 302
- an α-helix
Similar variants
- DCPS p.Arg152Ter Likely pathogenic ★★ same type
- DCPS p.Ala184Thr Uncertain significance ★★ ⚠ same type
- DCPS p.Arg145Cys Uncertain significance ★★ ⚠ same type
- DCPS p.Arg242Gly Uncertain significance ★★ ⚠ same type
- DCPS p.Pro235Leu Uncertain significance ★★ ⚠ same type
- DCPS p.Ala186= Benign/Likely benign ★★ same type
- DCPS p.Ala80= Likely benign ★★ same type
- DCPS p.Asp324= Likely benign ★★ 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/dcps-p-ile302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown