TPR p.Val1862=
c.5586C>T · rs367905191 · VCV748541
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00967%, nfe)
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 0.73 | GERP -2.5, phastCons 0.98 |
| Overall | ||
| CADD | 4.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00967%
European (non-Finnish) · 114/1,178,972 alleles
Filtering AF
0.00818%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00761%
Overall
0.00714%
115/1,611,226 alleles · very rare
exomes 110/1,459,132 · genomes 5/152,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00967% | 10,342 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,392 |
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.Val1862=
- Coding
- c.5586C>T
- MANE Select
- NM_003292
- dbSNP
- rs367905191
- Type
- single nucleotide variant
- Location
- chr1:186332213 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.60 · 4 PDB
- Residue 1862
- the 'sufficient and essential for mediating its nuclear import' region; the 'disordered' region
Similar variants
- TPR p.Thr1751Ala Uncertain significance ★★ ⚠ same type
- TPR p.Arg1832His Likely benign ★★ same type
- TPR p.Arg467= Benign/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-val1862 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown