POT1 p.Pro13fs
c.36_37dup · rs2485562891 · VCV2745977
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 7.729e-07)
Conditions
1
tumor predisposition syndrome 3
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 19 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.7 | GERP 1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
7.73e-05%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- POT1
- Protein
- p.Pro13fs
- Coding
- c.36_37dup
- MANE Select
- NM_015450
- dbSNP
- rs2485562891
- Type
- Microsatellite
- Location
- chr7:124892352 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 14 PDB
- Residue 13
- an α-helix
Similar variants
- POT1 p.Pro13Leu Uncertain significance ★★ ⚠ same residue
- POT1 p.Pro13= Likely benign ★★ same residue
- POT1 p.Pro13His Uncertain significance ★ ⚠ same residue
- POT1 p.Asn282_Ser283insTer Pathogenic ★★ same condition
- POT1 p.Pro190fs Pathogenic ★★ same condition
- POT1 p.Val285fs Pathogenic ★★ same condition
- POT1 p.Gln359del Uncertain significance ★★ same condition
- POT1 p.Met589fs Uncertain significance ★★ 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-pro13fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown