ESRP1 p.Ser404=
c.1212C>T · rs77276626 · VCV782036
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.6%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.148 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 12.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.6%
African / African-American · 1,938/74,454 alleles
Filtering AF
2.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.47%
Overall
0.258%
4,110/1,591,560 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.6% | 38 |
| Middle Eastern | 1.97% | 51 |
| Admixed American | 0.707% | 141 |
| Remaining individualsnot grpmax-eligible | 0.558% | 179 |
| European (non-Finnish) | 0.108% | 930 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0589% | 1,699 |
| South Asian | 0.0373% | 2,683 |
| Finnishnot grpmax-eligible | 0.00471% | 21,245 |
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
- ESRP1
- Protein
- p.Ser404=
- Coding
- c.1212C>T
- MANE Select
- NM_017697
- dbSNP
- rs77276626
- Type
- single nucleotide variant
- Location
- chr8:94668229 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.21 · 5 PDB
- Residue 404
- the rrm 2 domain; a β-strand
Similar variants
- ESRP1 c.133-10A>G Benign/Likely benign ★★ same type
- ESRP1 c.490+16T>C Benign ★★ same type
- ESRP1 c.589+10G>T Benign ★★ same type
- ESRP1 c.756-23T>C Benign ★★ same type
- ESRP1 p.Ala159Thr Likely benign ★★ same type
- ESRP1 p.Arg329= Likely benign ★★ same type
- ESRP1 p.Asn600= Benign ★★ same type
- ESRP1 p.Leu129= Benign ★★ 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/esrp1-p-ser404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown