TUBB2A p.Phe90=
c.270C>T · rs562003687 · VCV2139251
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, 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 -11 | GERP -3.7 |
| Overall | ||
| CADD | 10.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,854 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000496%
8/1,612,092 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,427 |
| African / African-American | 0.00267% | 37,471 |
| South Asian | 0.0011% | 90,818 |
| European (non-Finnish) | 0.000254% | 393,020 |
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
- TUBB2A
- Protein
- p.Phe90=
- Coding
- c.270C>T
- MANE Select
- NM_001069
- dbSNP
- rs562003687
- Type
- single nucleotide variant
- Location
- chr6:3155632 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 92.44 · 3 PDB
- Residue 90
- a β-strand
Similar variants
- TUBB2A p.Phe90Leu Uncertain significance ★ ⚠ same residue
- TUBB p.Asn52Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- TUBB p.Asp327Asn Pathogenic/Likely pathogenic ★★ same type
- TUBB p.Gln15His Likely pathogenic ★★ same type
- TUBB p.Glu111Lys Pathogenic/Likely pathogenic ★★ same type
- TUBB p.Glu401Lys Pathogenic ★★ same type
- TUBB p.Met299Val Pathogenic ★★ same type
- TUBB p.Thr221Ile Pathogenic/Likely pathogenic ★★ 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/tubb2a-p-phe90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown