TPR p.Arg467=
c.1399C>A · rs114751429 · VCV770683
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.927%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 13.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.927%
European (non-Finnish) · 10,920/1,178,356 alleles
Filtering AF
0.912%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.906%
Overall
0.747%
12,036/1,610,174 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.927% | 108 |
| Remaining individualsnot grpmax-eligible | 0.588% | 170 |
| Admixed American | 0.35% | 285 |
| Finnishnot grpmax-eligible | 0.286% | 349 |
| Middle Eastern | 0.281% | 356 |
| South Asian | 0.25% | 400 |
| African / African-American | 0.135% | 740 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0475% | 2,107 |
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
- TPR
- Protein
- p.Arg467=
- Coding
- c.1399C>A
- MANE Select
- NM_003292
- dbSNP
- rs114751429
- Type
- single nucleotide variant
- Location
- chr1:186358641 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.60 · 4 PDB
- Residue 467
- the 'necessary for association to the npc' region
Similar variants
- TPR p.Arg467Gln Uncertain significance ★ ⚠ same residue
- TPR p.Thr1751Ala Uncertain significance ★★ ⚠ same type
- TPR p.Arg1832His Likely benign ★★ same type
- TPR p.Leu1314= Benign ★★ same type
- TPR p.Pro2168Ser Benign ★★ same type
- TPR p.Thr762= Benign ★★ same type
- TPR c.2610+5G>A Uncertain significance ★ same type
- TPR p.Ala1025Thr 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/tpr-p-arg467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown