GFER p.Pro19=
c.57G>C · rs535377905 · VCV214469
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.14%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 5.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.14%
African / African-American · 1,454/67,988 alleles
Filtering AF
2.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.01%
Overall
0.113%
1,662/1,477,164 alleles · low-frequency
exomes 765/1,325,024 · genomes 897/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.14% | 47 |
| Middle Eastern | 0.193% | 517 |
| Admixed American | 0.184% | 544 |
| Remaining individualsnot grpmax-eligible | 0.172% | 582 |
| South Asian | 0.00258% | 38,741 |
| European (non-Finnish) | 0.00187% | 53,387 |
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
- GFER
- Protein
- p.Pro19=
- Coding
- c.57G>C
- MANE Select
- NM_005262
- dbSNP
- rs535377905
- Type
- single nucleotide variant
- Location
- chr16:1984275 (GRCh38)
- Gene constraint
- LOEUF 1.87 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.50 · 7 PDB
- Residue 19
- the 'disordered' region
Similar variants
- GFER p.Pro19Ser Uncertain significance ★★ ⚠ same residue
- GFER p.Pro19Leu Uncertain significance ★ ⚠ same residue
- GFER p.Arg194His Pathogenic ★★ same type
- GFER p.Ser189Ter Pathogenic ★★ same type
- GFER c.258+1G>A Uncertain significance ★★ same type
- GFER p.Ala45Thr Uncertain significance ★★ ⚠ same type
- GFER p.Ala46Val Uncertain significance ★★ ⚠ same type
- GFER p.Ala73Ser 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/gfer-p-pro19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown