ERF p.Tyr88=
c.264C>T · rs140522983 · VCV543071
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.056%, afr)
Conditions
1
TWIST1-related craniosynostosis
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 | GERP -3.7 |
| Overall | ||
| CADD | 1.752 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.056%
African / African-American · 42/75,034 alleles
Filtering AF
0.0425%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0378%
Overall
0.00471%
76/1,614,056 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.056% | 1,787 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| Admixed American | 0.015% | 6,668 |
| European (non-Finnish) | 0.000339% | 294,978 |
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.Tyr88=
- Coding
- c.264C>T
- MANE Select
- NM_006494
- dbSNP
- rs140522983
- Type
- single nucleotide variant
- Location
- chr19:42249936 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.46 · 2 PDB
- Residue 88
- a DNA-binding region; an α-helix
Similar variants
- ERF p.Arg183Ter Pathogenic ★★ same condition
- ERF p.Arg207Ter Pathogenic/Likely pathogenic ★★ same condition
- ERF p.Arg218Ter Pathogenic/Likely pathogenic ★★ same condition
- ERF p.Arg86Cys Pathogenic/Likely pathogenic ★★ same condition
- ERF p.Ser24Ter Pathogenic/Likely pathogenic ★★ same condition
- ERF p.Arg458Gly Uncertain significance ★★ ⚠ same condition
- ERF p.Arg493His Uncertain significance ★★ ⚠ same condition
- ERF p.Lys401Glu 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/erf-p-tyr88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown