GDF3 p.Ala62=
c.186G>A · rs752330502 · VCV1081207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00445%, eas)
Conditions
1
Klippel-Feil syndrome 3, autosomal dominant
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 -2.3 | |
| Overall | ||
| CADD | 3.222 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
East Asian · 2/44,898 alleles
Filtering AF
0.000738%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000805%
13/1,613,966 alleles · very rare
exomes 11/1,461,828 · genomes 2/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00445% | 22,449 |
| Admixed American | 0.00333% | 29,993 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00267% | 37,452 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.000339% | 294,998 |
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
- GDF3
- Protein
- p.Ala62=
- Coding
- c.186G>A
- MANE Select
- NM_020634
- dbSNP
- rs752330502
- Type
- single nucleotide variant
- Location
- chr12:7695543 (GRCh38)
- Gene constraint
- LOEUF 1.513 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.72
Similar variants
- GDF3 p.Ala62Gly Uncertain significance ★ ⚠ same residue
- GDF3 p.Arg274Trp Uncertain significance ★★ ⚠ same condition
- GDF3 p.Ser304Pro Uncertain significance ★★ ⚠ same condition
- GDF3 p.Val320Ile Uncertain significance ★★ ⚠ same condition
- GDF3 p.Arg195Trp Benign/Likely benign ★★ same condition
- GDF3 p.Asn193= Benign/Likely benign ★★ same condition
- GDF3 p.Gly213Arg Benign/Likely benign ★★ same condition
- GDF3 p.Leu305Pro 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/gdf3-p-ala62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown