Is POT1 p.Ser507Phe (c.1520C>T) pathogenic?

POT1 p.Ser507Phe (c.1520C>T) is classified Uncertain significance in POT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-13). AlphaMissense: likely pathogenic (0.873); Very rare (popmax 8.72e-05%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with POT1 p.Ser507Phe (c.1520C>T)?

POT1 p.Ser507Phe (c.1520C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is POT1 p.Ser507Phe (c.1520C>T) in the general population?

POT1 p.Ser507Phe (c.1520C>T) is very rare (popmax 8.72e-05%, nfe) (gnomAD).

What do computational predictors say about POT1 p.Ser507Phe (c.1520C>T)?

AlphaMissense predicts likely pathogenic (score 0.873) — an in-silico prediction, not a clinical call.

POT1 p.Ser507Phe

c.1520C>T · rs2485352818 · VCV1774416

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.873 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.72e-05%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.873	likely pathogenic
REVEL	0.402	indeterminate
SaProt	LLR -10.82	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 29 kb · p 0.48 · regional, not allelic
Overall
CADD	26.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.72e-05% European (non-Finnish) · 1/1,147,438 alleles

Overall 6.34e-05% 1/1,576,814 alleles · very rare exomes 1/1,424,634 · genomes 0/152,180 · 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.Ser507Phe
Coding: c.1520C>T
MANE Select: NM_015450
dbSNP: rs2485352818
Type: single nucleotide variant
Location: chr7:124829328 (GRCh38)
Gene constraint: LOEUF 0.871 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 87.63 · 14 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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
POT1 c.1506-1G>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-ser507phe (accessed [today's date]).

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