ESRP2 p.Thr475=
c.1425G>A · rs56323755 · VCV780184
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.78%, afr)
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 -1.9 | GERP -5.7 |
| Overall | ||
| CADD | 7.604 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.78%
African / African-American · 1,332/75,020 alleles
Filtering AF
1.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.66%
Overall
0.0954%
1,540/1,614,068 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.78% | 56 |
| Admixed American | 0.155% | 645 |
| Remaining individualsnot grpmax-eligible | 0.109% | 919 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.0264% | 3,795 |
| East Asian | 0.00223% | 44,868 |
| European (non-Finnish) | 0.00144% | 69,411 |
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
- ESRP2
- Protein
- p.Thr475=
- Coding
- c.1425G>A
- MANE Select
- NM_024939
- dbSNP
- rs56323755
- Type
- single nucleotide variant
- Location
- chr16:68231569 (GRCh38)
- Gene constraint
- LOEUF 0.753 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.87
- Residue 475
- the rrm 3 domain
Similar variants
- ESRP2 p.Gly122Arg Uncertain significance ★★ ⚠ same type
- ESRP2 p.Gly463Glu Uncertain significance ★★ ⚠ same type
- ESRP2 p.Leu681Phe Uncertain significance ★★ ⚠ same type
- ESRP2 p.Ala691Thr Benign ★★ same type
- ESRP2 p.Ala20Pro Uncertain significance ★ ⚠ same type
- ESRP2 p.Ala273Val Uncertain significance ★ ⚠ same type
- ESRP2 p.Ala322Thr Uncertain significance ★ ⚠ same type
- ESRP2 p.Ala322Val 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/esrp2-p-thr475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown