DCPS p.Pro239=
c.717G>A · rs79514900 · VCV732989
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.312%, afr)
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 -8.3 | GERP -5.8 |
| Overall | ||
| CADD | 0.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.312%
African / African-American · 234/75,030 alleles
Filtering AF
0.279%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.266%
Overall
0.0154%
249/1,613,750 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.312% | 321 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,928 |
| Admixed American | 0.00667% | 14,997 |
| European (non-Finnish) | 0.000339% | 294,971 |
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.Pro239=
- Coding
- c.717G>A
- MANE Select
- NM_014026
- dbSNP
- rs79514900
- Type
- single nucleotide variant
- Location
- chr11:126343387 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.18 · 11 PDB
- Residue 239
- an α-helix
Similar variants
- DCPS p.Pro239Leu Uncertain significance ★ ⚠ same residue
- DCPS p.Pro239Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown