TPRN p.Pro142=
c.426G>T · rs1478692998 · VCV2888982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0342%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -1.6 |
| Overall | ||
| CADD | 6.253 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0342%
African / African-American · 19/55,578 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0186%
Overall
0.00203%
20/986,182 alleles · ultra-rare
exomes 9/843,614 · genomes 11/142,568 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0342% | 2,925 |
| Admixed American | 0.00627% | 15,938 |
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.Pro142=
- Coding
- c.426G>T
- MANE Select
- NM_001128228
- dbSNP
- rs1478692998
- Type
- single nucleotide variant
- Location
- chr9:137200286 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.27 · 1 PDB
- Residue 142
- the 'disordered' region
Similar variants
- TPRN p.Pro142Leu 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
- TPRN p.Arg231Trp 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-pro142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown