ERF p.Pro472=
c.1416C>T · VCV4942572
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0661%, 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 -16 | GERP -3 |
| Overall | ||
| CADD | 0.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0661%
Middle Eastern · 4/6,056 alleles
Filtering AF
0.0226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.0123%
198/1,611,388 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0661% | 1,514 |
| South Asian | 0.0297% | 3,369 |
| European (non-Finnish) | 0.0135% | 7,410 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,472 |
| East Asian | 0.00223% | 44,796 |
| Admixed American | 0.00167% | 59,918 |
| African / African-American | 0.00133% | 75,004 |
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
- ERF
- Protein
- p.Pro472=
- Coding
- c.1416C>T
- MANE Select
- NM_006494
- Type
- single nucleotide variant
- Location
- chr19:42248696 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.46 · 2 PDB
- Residue 472
- the 'disordered' region
Similar variants
- ERF p.Pro472Ser Uncertain significance ★ ⚠ same residue
- ERF p.Arg183Ter Pathogenic ★★ same type
- ERF p.Arg207Ter Pathogenic/Likely pathogenic ★★ same type
- ERF p.Arg218Ter Pathogenic/Likely pathogenic ★★ same type
- ERF p.Arg233Ter Pathogenic ★★ same type
- ERF p.Arg86Cys Pathogenic/Likely pathogenic ★★ same type
- ERF p.Gln263Ter Pathogenic ★★ same type
- ERF p.Gly53Arg Likely pathogenic ★★ 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/erf-p-pro472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown