ESR2 p.Arg501=
c.1503C>T · rs1481617898 · VCV2961030
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, 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 -8.7 | GERP -5.8 |
| Overall | ||
| CADD | 0.433 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,890 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00062%
10/1,614,008 alleles · very rare
exomes 6/1,461,886 · genomes 4/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,482 |
| South Asian | 0.0011% | 91,074 |
| European (non-Finnish) | 0.000254% | 393,345 |
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
- ESR2
- Protein
- p.Arg501=
- Coding
- c.1503C>T
- MANE Select
- NM_001437
- dbSNP
- rs1481617898
- Type
- single nucleotide variant
- Location
- chr14:64233227 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.76 · 39 PDB
- Residue 501
- an α-helix
Similar variants
- ESR2 p.Ala432Thr Uncertain significance ★★ ⚠ same type
- ESR2 p.Arg230Gln Uncertain significance ★★ ⚠ same type
- ESR2 p.Arg346Cys Uncertain significance ★★ ⚠ same type
- ESR2 p.Arg388Gln Uncertain significance ★★ ⚠ same type
- ESR2 p.Asn407Ser Uncertain significance ★★ ⚠ same type
- ESR2 p.Asp154Asn Uncertain significance ★★ ⚠ same type
- ESR2 p.Cys169Phe Uncertain significance ★★ ⚠ same type
- ESR2 p.Gly243Asp 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/esr2-p-arg501 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown