GDF1 p.Ser119=
c.357G>A · rs758878687 · VCV695263
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.297%, mid)
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 0.25 | GERP -2.5, phastCons 0.004 |
| Overall | ||
| CADD | 6.121 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.297%
Middle Eastern · 13/4,376 alleles
Filtering AF
0.176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.139%
Overall
0.0326%
500/1,532,044 alleles · rare
exomes 474/1,380,132 · genomes 26/151,912 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.297% | 337 |
| European (non-Finnish) | 0.0384% | 2,606 |
| Admixed American | 0.0313% | 3,195 |
| Remaining individualsnot grpmax-eligible | 0.0268% | 3,732 |
| Finnishnot grpmax-eligible | 0.0249% | 4,009 |
| South Asian | 0.00357% | 27,989 |
| African / African-American | 0.00138% | 72,362 |
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
- GDF1
- Protein
- p.Ser119=
- Coding
- c.357G>A
- MANE Select
- NM_001492
- dbSNP
- rs758878687
- Type
- single nucleotide variant
- Location
- chr19:18869359 (GRCh38)
- Gene constraint
- LOEUF 1.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.44
Similar variants
- GDF1 p.Ser119Leu Uncertain significance ★★ ⚠ same residue
- CERS1 p.His233Arg Uncertain significance ★★ ⚠ same type
- CERS1 p.His236Gln Uncertain significance ★★ same type
- CERS1 p.Lys98Arg Uncertain significance ★★ ⚠ same type
- CERS1 p.Pro140Leu Uncertain significance ★★ ⚠ same type
- CERS1 p.Pro260Leu Uncertain significance ★★ ⚠ same type
- CERS1 p.Pro84Thr Uncertain significance ★★ same type
- CERS1 p.Ser330Ile Uncertain significance ★★ ⚠ same type
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/gdf1-p-ser119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown