INO80 p.Phe1069=
c.3207C>T · VCV4924302
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 3 | GERP 0.047, phastCons 1 |
| Overall | ||
| CADD | 7.717 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,020 alleles
Overall
0.000248%
4/1,614,134 alleles · very rare
exomes 4/1,461,864 · genomes 0/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,020 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| South Asian | 0.0011% | 91,078 |
| European (non-Finnish) | 8.47e-05% | 1,180,012 |
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
- INO80
- Protein
- p.Phe1069=
- Coding
- c.3207C>T
- MANE Select
- NM_017553
- Type
- single nucleotide variant
- Location
- chr15:41020967 (GRCh38)
- Gene constraint
- LOEUF 0.165 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.05 · 6 PDB
- Residue 1069
- the 'assembles ino80 complex module consisting of conserved components ino80b, ino80c, actr5, rvbl1, rvbl2' region
Similar variants
- INO80 p.Phe1069Leu Uncertain significance ★ ⚠ same residue
- INO80 p.Ala1340Pro Uncertain significance ★★ ⚠ same type
- INO80 p.Ala1388Pro Uncertain significance ★★ ⚠ same type
- INO80 p.Arg1029Gly Uncertain significance ★★ ⚠ same type
- INO80 p.Leu906Val Uncertain significance ★★ ⚠ same type
- INO80 c.2070+12T>A Likely benign ★★ same type
- INO80 c.2577-17A>T Benign ★★ same type
- INO80 p.Ala325= Benign ★★ 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/ino80-p-phe1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown