ESPL1 p.Phe9=
c.27T>C · rs142528308 · VCV3035030
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.122%, sas)
Conditions
1
ESPL1-related disorder
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 -0.07 | GERP -2.4, phastCons 0.87 |
| Overall | ||
| CADD | 10.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.122%
South Asian · 111/90,690 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0969%
Overall
0.00843%
136/1,612,622 alleles · rare
exomes 126/1,460,366 · genomes 10/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.122% | 817 |
| Middle Eastern | 0.0166% | 6,040 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,925 |
| European (non-Finnish) | 0.00144% | 69,380 |
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
- ESPL1
- Protein
- p.Phe9=
- Coding
- c.27T>C
- MANE Select
- NM_012291
- dbSNP
- rs142528308
- Type
- single nucleotide variant
- Location
- chr12:53268793 (GRCh38)
- Gene constraint
- LOEUF 0.292 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.67 · 9 PDB
Disease context
ESPL1-related disorder
Similar variants
- ESPL1 p.Ser1239Ter Uncertain significance ★ same condition
- ESPL1 c.6161+7C>T Likely benign same condition
- ESPL1 p.Ala116Val Benign same condition
- ESPL1 p.Ala1438= Likely benign same condition
- ESPL1 p.Arg1318Gln Likely benign same condition
- ESPL1 p.Asn1723= Likely benign same condition
- ESPL1 p.Asp1351= Likely benign same condition
- ESPL1 p.Gly1510Arg Likely benign same condition
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/espl1-p-phe9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown