POT1 p.Phe470=
c.1410T>C · VCV3308956
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
hereditary neoplastic syndrome
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 4.6 | GERP -0.64, phastCons 1 |
| Overall | ||
| CADD | 9.495 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,810 alleles
Overall
6.2e-05%
1/1,613,960 alleles · very rare
exomes 1/1,461,620 · genomes 0/152,340 · joint denominator
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
- POT1
- Protein
- p.Phe470=
- Coding
- c.1410T>C
- MANE Select
- NM_015450
- Type
- single nucleotide variant
- Location
- chr7:124835374 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 14 PDB
- Residue 470
- a β-strand
Similar variants
- POT1 p.Phe470Leu Uncertain significance ★ ⚠ same residue
- POT1 c.10-2A>C Pathogenic/Likely pathogenic ★★ same condition
- POT1 c.1163+1G>A Likely pathogenic ★★ same condition
- POT1 c.1164-1G>A Pathogenic/Likely pathogenic ★★ same condition
- POT1 c.124+1G>C Pathogenic/Likely pathogenic ★★ same condition
- POT1 c.124+2T>C Likely pathogenic ★★ same condition
- POT1 c.125-2A>G Likely pathogenic ★★ same condition
- POT1 c.1369+1G>A Likely pathogenic ★★ same condition
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/pot1-p-phe470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown