EZR p.Pro265=
c.795T>G · rs147363431 · VCV435110
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.183%, nfe)
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 -5.3 | GERP -4.3 |
| Overall | ||
| CADD | 3.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.183%
European (non-Finnish) · 2,155/1,177,336 alleles
Filtering AF
0.177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.174%
Overall
0.142%
2,281/1,611,216 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.183% | 546 |
| Remaining individualsnot grpmax-eligible | 0.0705% | 1,419 |
| Admixed American | 0.035% | 2,858 |
| South Asian | 0.0341% | 2,936 |
| Middle Eastern | 0.0331% | 3,025 |
| African / African-American | 0.0253% | 3,947 |
| Finnishnot grpmax-eligible | 0.0125% | 8,004 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,588 |
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
- EZR
- Protein
- p.Pro265=
- Coding
- c.795T>G
- MANE Select
- NM_001111077
- dbSNP
- rs147363431
- Type
- single nucleotide variant
- Location
- chr6:158776408 (GRCh38)
- Gene constraint
- LOEUF 0.697 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.16 · 7 PDB
- Residue 265
- the ferm domain; the 'interaction with scyl3' region
Similar variants
- EZR p.Ala494Val Uncertain significance ★★ ⚠ same type
- EZR p.Arg381Gln Uncertain significance ★★ ⚠ same type
- EZR p.Thr533Met Uncertain significance ★★ ⚠ same type
- EZR p.Asn251Ser Likely benign ★★ same type
- EZR p.Glu377= Benign/Likely benign ★★ same type
- EZR p.Pro474= Likely benign ★★ same type
- EZR p.Tyr354= Benign ★★ same type
- EZR c.959+7G>A Conflicting classifications of pathogenicity ★ 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/ezr-p-pro265 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown