GDF2 p.Thr239=
c.717G>A · rs781821989 · VCV1587300
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, afr)
Conditions
2
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 -0.064 | GERP -5.9, phastCons 0.017 |
| Overall | ||
| CADD | 4.049 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,894 alleles
Filtering AF
0.00922%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.00167%
27/1,613,898 alleles · ultra-rare
exomes 23/1,461,786 · genomes 4/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,241 |
| East Asian | 0.00446% | 22,437 |
| South Asian | 0.00329% | 30,360 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| European (non-Finnish) | 0.000678% | 147,504 |
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.Thr239=
- Coding
- c.717G>A
- MANE Select
- NM_016204
- dbSNP
- rs781821989
- Type
- single nucleotide variant
- Location
- chr10:47325211 (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.Thr239Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- GDF2 p.Arg110Gln Likely pathogenic ★★ same condition
- GDF2 p.Gln26Ter Pathogenic ★★ same condition
- GDF2 p.Glu355Ter Pathogenic/Likely pathogenic ★★ same condition
- GDF2 p.Trp214Ter Pathogenic/Likely pathogenic ★★ same condition
- GDF2 p.Val423Met Pathogenic/Likely pathogenic ★★ same condition
- GDF2 p.Ala105Gly Uncertain significance ★★ ⚠ same condition
- GDF2 p.Arg213Cys Uncertain significance ★★ ⚠ 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-thr239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown