Is POT1 p.Pro13= (c.39C>T) pathogenic?

POT1 p.Pro13= (c.39C>T) is classified Likely benign in POT1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-01). Very rare (popmax 0.00527%, amr); Associated with tumor predisposition syndrome 3.

What condition is associated with POT1 p.Pro13= (c.39C>T)?

POT1 p.Pro13= (c.39C>T) is associated with tumor predisposition syndrome 3, hereditary neoplastic syndrome (ClinVar).

How common is POT1 p.Pro13= (c.39C>T) in the general population?

POT1 p.Pro13= (c.39C>T) is very rare (popmax 0.00527%, amr) (gnomAD).

POT1 p.Pro13=

c.39C>T · rs544201070 · VCV753709

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00527%, amr)

Conditions

tumor predisposition syndrome 3

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 -0.23	GERP -3.5, phastCons 0.032
Overall
CADD	7.023	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00527% Admixed American · 2/37,922 alleles

Filtering AF 0.000874% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000327%

Overall 0.000266% 4/1,503,050 alleles · very rare exomes 1/1,351,522 · genomes 3/151,528 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00527%	18,961
East Asian	0.00264%	37,928
Remaining individualsnot grpmax-eligible	0.00174%	57,616

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.Pro13=
Coding: c.39C>T
MANE Select: NM_015450
dbSNP: rs544201070
Type: single nucleotide variant
Location: chr7:124892351 (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

Full POT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

tumor predisposition syndrome 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

Similar variants

POT1 p.Pro13Leu Uncertain significance ★★ ⚠ same residue
POT1 p.Pro13Ser Uncertain significance ★★ ⚠ same residue
POT1 p.Pro13His Uncertain significance ★ ⚠ same residue
POT1 p.Pro13fs Pathogenic ★ 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

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-pro13 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown