ESYT2 p.Arg5Pro
c.14G>C · VCV4665496
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00041%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.015 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -1 |
| Regional constraint | o/e 0.93 | unconstrained · MANE · 95 kb · p 0.024 · regional, not allelic |
| Overall | ||
| CADD | 15.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00041%
European (non-Finnish) · 4/974,688 alleles
Filtering AF
9.6e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.5e-05%
Overall
0.00038%
4/1,052,964 alleles · very rare
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
- ESYT2
- Protein
- p.Arg5Pro
- Coding
- c.14G>C
- MANE Select
- NM_001367773
- Type
- single nucleotide variant
- Location
- chr7:158829405 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.44 · 4 PDB
- Residue 5
- the 'disordered' region
Similar variants
- ESYT2 p.Arg5Gln Uncertain significance ★ same residue
- ESYT2 c.26C>T Uncertain significance ★ same type
- ESYT2 c.43C>G Uncertain significance ★ same type
- ESYT2 c.-17C>G Uncertain significance ★ same type
- ESYT2 c.-38C>T Uncertain significance ★ ⚠ same type
- ESYT2 c.-41A>C Uncertain significance ★ ⚠ same type
- ESYT2 c.-55C>G Uncertain significance ★ same type
- ESYT2 c.-59G>A 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/esyt2-p-arg5pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown