TPRN p.Ser288=
c.864C>T · VCV4801573
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.321%, 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 -1 | GERP -1.9 |
| Overall | ||
| CADD | 2.802 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.321%
East Asian · 135/42,106 alleles
Filtering AF
0.277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.26%
Overall
0.00869%
136/1,564,574 alleles · rare
exomes 129/1,412,360 · genomes 7/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.321% | 312 |
| Remaining individualsnot grpmax-eligible | 0.00165% | 60,636 |
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
- TPRN
- Protein
- p.Ser288=
- Coding
- c.864C>T
- MANE Select
- NM_001128228
- Type
- single nucleotide variant
- Location
- chr9:137199848 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.27 · 1 PDB
- Residue 288
- the 'disordered' region
Similar variants
- TPRN p.Ser288Phe Uncertain significance ★★ ⚠ same residue
- TPRN p.Ser288Tyr Uncertain significance ★ ⚠ same residue
- TPRN p.Gln414Ter Pathogenic ★★ same type
- TPRN c.1725+5G>A Uncertain significance ★★ same type
- TPRN p.Ala191Val Uncertain significance ★★ ⚠ same type
- TPRN p.Ala302Asp Uncertain significance ★★ ⚠ same type
- TPRN p.Ala390Ser Uncertain significance ★★ ⚠ same type
- TPRN p.Ala695Thr 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/tprn-p-ser288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown