GDF2 p.Lys221=
c.663G>A · rs782726443 · VCV1754626
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
Cardiovascular phenotype
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 -0.54 | GERP -5.6, phastCons 0.001 |
| Overall | ||
| CADD | 1.781 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,046 alleles
Overall
6.2e-05%
1/1,613,842 alleles · very rare
exomes 0/1,461,658 · genomes 1/152,184 · joint denominator
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
- GDF2
- Protein
- p.Lys221=
- Coding
- c.663G>A
- MANE Select
- NM_016204
- dbSNP
- rs782726443
- Type
- single nucleotide variant
- Location
- chr10:47325157 (GRCh38)
- Gene constraint
- LOEUF 1.208 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.79 · 20 PDB
Similar variants
- GDF2 p.Ala105Gly Uncertain significance ★★ ⚠ same condition
- GDF2 p.Arg333Gln Uncertain significance ★★ ⚠ same condition
- GDF2 p.Gly247Val Uncertain significance ★★ ⚠ same condition
- GDF2 p.Ala105= Likely benign ★★ same condition
- GDF2 p.Ala310= Likely benign ★★ same condition
- GDF2 p.Ala365= Likely benign ★★ same condition
- GDF2 p.Arg319= Likely benign ★★ same condition
- GDF2 p.Asn259Ser Benign/Likely benign ★★ same condition
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/gdf2-p-lys221 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown