TPX2 p.Ser94=
c.282C>T · rs115949457 · VCV785652
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.97%, afr)
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 -2.6 | GERP -5.4 |
| Overall | ||
| CADD | 0.646 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.97%
African / African-American · 2,969/74,866 alleles
Filtering AF
3.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.8%
Overall
0.203%
3,269/1,613,472 alleles · low-frequency
exomes 1,592/1,461,576 · genomes 1,677/151,896 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.97% | 25 |
| Remaining individualsnot grpmax-eligible | 0.234% | 428 |
| Admixed American | 0.209% | 479 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.00659% | 15,168 |
| European (non-Finnish) | 0.00144% | 69,403 |
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
- TPX2
- Protein
- p.Ser94=
- Coding
- c.282C>T
- MANE Select
- NM_012112
- dbSNP
- rs115949457
- Type
- single nucleotide variant
- Location
- chr20:31766608 (GRCh38)
- Gene constraint
- LOEUF 0.29 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.23 · 14 PDB
Similar variants
- TPX2 p.Ala184= Benign ★★ same type
- TPX2 p.Ala142Val Uncertain significance ★ ⚠ same type
- TPX2 p.Ala184Gly Uncertain significance ★ ⚠ same type
- TPX2 p.Ala668Val Uncertain significance ★ same type
- TPX2 p.Ala683Pro Uncertain significance ★ ⚠ same type
- TPX2 p.Arg229Trp Uncertain significance ★ ⚠ same type
- TPX2 p.Arg267Gln Uncertain significance ★ ⚠ same type
- TPX2 p.Arg296Gln Uncertain significance ★ ⚠ 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/tpx2-p-ser94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown