ESR1 p.Leu39=
c.115C>T · rs781772511 · VCV2656999
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 3.2 | GERP 0.67, phastCons 1 |
| Overall | ||
| CADD | 13.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ESR1
- Protein
- p.Leu39=
- Coding
- c.115C>T
- MANE Select
- NM_000125
- dbSNP
- rs781772511
- Type
- single nucleotide variant
- Location
- chr6:151808027 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.14 · 492 PDB
- Residue 39
- the 'modulating (transactivation af-1); mediates interaction with macrod1' region; the 'interaction with ddx5; self-association' region; the 'required for interaction with ncoa1' region
Similar variants
- SYNE1 p.Arg8746Ter Pathogenic/Likely pathogenic ★★ same type
- ESR1 p.Lys299Arg Uncertain significance ★★ ⚠ same type
- SYNE1 p.Arg8735Leu Uncertain significance ★★ ⚠ same type
- SYNE1 p.Arg8738His Uncertain significance ★★ ⚠ same type
- SYNE1 p.Arg8746Gln Uncertain significance ★★ same type
- SYNE1 p.Arg8782Gln Uncertain significance ★★ same type
- SYNE1 p.Arg8782Gly Uncertain significance ★★ same type
- SYNE1 p.Asp8725Asn 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/esr1-p-leu39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown