TPX2 p.Lys439=
c.1317A>G · rs148051312 · VCV769085
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.786%, 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 0.32 | GERP -3.3, phastCons 0.58 |
| Overall | ||
| CADD | 3.951 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.786%
African / African-American · 589/74,890 alleles
Filtering AF
0.734%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.713%
Overall
0.0456%
735/1,612,338 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.786% | 127 |
| Remaining individualsnot grpmax-eligible | 0.0913% | 1,095 |
| Admixed American | 0.0555% | 1,802 |
| Middle Eastern | 0.0165% | 6,060 |
| European (non-Finnish) | 0.00449% | 22,258 |
| South Asian | 0.00221% | 45,219 |
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.Lys439=
- Coding
- c.1317A>G
- MANE Select
- NM_012112
- dbSNP
- rs148051312
- Type
- single nucleotide variant
- Location
- chr20:31783825 (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.Ser94= 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
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-lys439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown