DEDD2 p.Cys207=
c.621C>T · VCV3898092
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.75%, mid)
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 -0.66 | GERP -3.3 |
| Overall | ||
| CADD | 9.866 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.75%
Middle Eastern · 106/6,048 alleles
Filtering AF
1.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.38%
Overall
1.14%
18,333/1,602,140 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.75% | 57 |
| European (non-Finnish) | 1.35% | 74 |
| Amishnot grpmax-eligible | 1.1% | 91 |
| Remaining individualsnot grpmax-eligible | 0.912% | 110 |
| Finnishnot grpmax-eligible | 0.874% | 114 |
| South Asian | 0.719% | 139 |
| Admixed American | 0.508% | 197 |
| Ashkenazi Jewishnot grpmax-eligible | 0.352% | 284 |
| African / African-American | 0.237% | 422 |
| East Asian | 0.0136% | 7,352 |
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
- DEDD2
- Protein
- p.Cys207=
- Coding
- c.621C>T
- MANE Select
- NM_133328
- Type
- single nucleotide variant
- Location
- chr19:42199798 (GRCh38)
- Gene constraint
- LOEUF 1.12 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.80
Similar variants
- DEDD2 p.Ala103Glu Uncertain significance ★ ⚠ same type
- DEDD2 p.Ala177Val Uncertain significance ★ ⚠ same type
- DEDD2 p.Ala52Val Uncertain significance ★ ⚠ same type
- DEDD2 p.Arg114Cys Uncertain significance ★ ⚠ same type
- DEDD2 p.Arg131Cys Uncertain significance ★ ⚠ same type
- DEDD2 p.Arg132Cys Uncertain significance ★ ⚠ same type
- DEDD2 p.Arg132His Uncertain significance ★ ⚠ same type
- DEDD2 p.Arg156Gln 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/dedd2-p-cys207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown