ESX1 p.Pro289=
c.867A>G · rs782815788 · VCV2661113
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.116%, eas)
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 -0.21 | GERP -1.1 |
| Overall | ||
| CADD | 2.915 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
East Asian · 38/32,719 alleles
Filtering AF
0.087%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0768%
Overall
0.006%
70/1,166,564 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.116% | 861 |
| Middle Eastern | 0.025% | 4,007 |
| South Asian | 0.0158% | 6,343 |
| Remaining individualsnot grpmax-eligible | 0.0087% | 11,492 |
| Admixed American | 0.00236% | 42,358 |
| European (non-Finnish) | 0.00206% | 48,477 |
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
- ESX1
- Protein
- p.Pro289=
- Coding
- c.867A>G
- MANE Select
- NM_153448
- dbSNP
- rs782815788
- Type
- single nucleotide variant
- Location
- chrX:104250582 (GRCh38)
- Structure
- AlphaFold pLDDT 62.35
- Residue 289
- the '15 x 9 aa tandem repeats of p-p-x-x-p-x-p-p-x' region
Similar variants
- ESX1 p.Pro289Ser Likely benign ★ ⚠ same residue
- ESX1 p.Pro320Arg Benign ★★ same type
- ESX1 p.Trp297Gly Likely benign ★★ same type
- ESX1 p.Pro365Arg Likely pathogenic ★ ⚠ same type
- ESX1 p.Ala292Val Uncertain significance ★ ⚠ same type
- ESX1 p.Ala301Thr Uncertain significance ★ ⚠ same type
- ESX1 p.Ala319Val Uncertain significance ★ ⚠ same type
- ESX1 p.Ala337Glu 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/esx1-p-pro289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown