GDF2 p.Lys286=
c.858G>A · rs1369185858 · VCV1763947
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 0.93 | GERP -1.7, phastCons 0.36 |
| Overall | ||
| CADD | 4.082 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,934 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000372%
6/1,614,112 alleles · very rare
exomes 4/1,461,878 · genomes 2/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,467 |
| Admixed American | 0.00167% | 60,012 |
| European (non-Finnish) | 0.000254% | 393,354 |
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.Lys286=
- Coding
- c.858G>A
- MANE Select
- NM_016204
- dbSNP
- rs1369185858
- Type
- single nucleotide variant
- Location
- chr10:47325352 (GRCh38)
- Gene constraint
- LOEUF 1.208 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.79 · 20 PDB
- Residue 286
- the 'disordered' region
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-lys286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown