GDF2 p.Phe112=
c.336C>T · VCV3709435
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000126%)
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 7.6 | GERP 2.9, phastCons 1 |
| Overall | ||
| CADD | 13.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000126%
Overall
0.000126%
2/1,593,004 alleles · very rare
exomes 1/1,440,820 · 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.Phe112=
- Coding
- c.336C>T
- MANE Select
- NM_016204
- Type
- single nucleotide variant
- Location
- chr10:47323004 (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.Phe112Leu Uncertain significance ★ ⚠ 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-phe112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown