TUBB2A p.Pro243=
c.729G>A · rs771262137 · VCV1445273
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00227%, 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 -20 | GERP -4.1 |
| Overall | ||
| CADD | 0.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00227%
East Asian · 1/44,142 alleles
Filtering AF
0.000369%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000138%
Overall
0.000627%
10/1,594,242 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00227% | 44,142 |
| South Asian | 0.00222% | 44,988 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,154 |
| African / African-American | 0.00142% | 70,184 |
| European (non-Finnish) | 0.000426% | 234,528 |
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.Pro243=
- Coding
- c.729G>A
- MANE Select
- NM_001069
- dbSNP
- rs771262137
- Type
- single nucleotide variant
- Location
- chr6:3154472 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 92.44 · 3 PDB
Similar variants
- TUBB2A p.Pro243Arg Uncertain significance ★ ⚠ same residue
- TUBB2A p.Pro243Leu Conflicting classifications of pathogenicity ★ ⚠ 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
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-pro243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown