TUBB2A p.Ser413=
c.1239C>T · rs2113784943 · VCV1535595
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, 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 9.8 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 13.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,178,620 alleles
Overall
6.21e-05%
1/1,609,860 alleles · very rare
exomes 1/1,460,602 · genomes 0/149,258 · joint denominator
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.Ser413=
- Coding
- c.1239C>T
- MANE Select
- NM_001069
- dbSNP
- rs2113784943
- Type
- single nucleotide variant
- Location
- chr6:3153962 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 92.44 · 3 PDB
- Residue 413
- an α-helix
Similar variants
- 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
- TUBB p.Val353Ile 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-ser413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown