TTK p.Pro410=
c.1230G>A · rs16891423 · VCV788996
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.72%, 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 0.35 | GERP -2.8, phastCons 0.55 |
| Overall | ||
| CADD | 8.246 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.72%
African / African-American · 2,788/75,014 alleles
Filtering AF
3.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.55%
Overall
0.203%
3,274/1,613,714 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.72% | 27 |
| Remaining individualsnot grpmax-eligible | 0.275% | 363 |
| Admixed American | 0.22% | 454 |
| Middle Eastern | 0.182% | 551 |
| East Asian | 0.029% | 3,449 |
| European (non-Finnish) | 0.0129% | 7,762 |
| South Asian | 0.0066% | 15,159 |
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
- TTK
- Protein
- p.Pro410=
- Coding
- c.1230G>A
- MANE Select
- NM_003318
- dbSNP
- rs16891423
- Type
- single nucleotide variant
- Location
- chr6:80022445 (GRCh38)
- Gene constraint
- LOEUF 0.666 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.11 · 78 PDB
- Residue 410
- the 'disordered' region
Similar variants
- TTK p.Pro410Leu Uncertain significance ★ ⚠ same residue
- TTK p.Thr423= Likely benign ★★ same type
- TTK p.Ala110Pro Uncertain significance ★ ⚠ same type
- TTK p.Ala251Gly Uncertain significance ★ ⚠ same type
- TTK p.Ala401Pro Uncertain significance ★ ⚠ same type
- TTK p.Ala402Val Uncertain significance ★ ⚠ same type
- TTK p.Ala787Gly Uncertain significance ★ ⚠ same type
- TTK p.Arg129Cys 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/ttk-p-pro410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown