TPRN p.Pro419=
c.1257G>A · rs139972044 · VCV2699492
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0153%, amr)
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 -3 | GERP -1.5 |
| Overall | ||
| CADD | 1.483 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0153%
Admixed American · 9/58,924 alleles
Filtering AF
0.00796%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00588%
Overall
0.00168%
27/1,604,314 alleles · ultra-rare
exomes 22/1,451,950 · genomes 5/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0153% | 6,547 |
| East Asian | 0.00675% | 14,811 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,054 |
| Finnishnot grpmax-eligible | 0.00163% | 61,440 |
| African / African-American | 0.00134% | 74,890 |
| European (non-Finnish) | 0.000935% | 106,922 |
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.Pro419=
- Coding
- c.1257G>A
- MANE Select
- NM_001128228
- dbSNP
- rs139972044
- Type
- single nucleotide variant
- Location
- chr9:137199455 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.27 · 1 PDB
- Residue 419
- the 'disordered' region
Similar variants
- TPRN p.Pro419Leu Benign/Likely benign ★★ 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-pro419 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown