Is POT1 p.Val391Phe (c.1171G>T) pathogenic?

POT1 p.Val391Phe (c.1171G>T) is classified Uncertain significance in POT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-10). AlphaMissense: likely benign (0.2665); Absent from gnomAD v4.1; Associated with tumor predisposition syndrome 3.

What condition is associated with POT1 p.Val391Phe (c.1171G>T)?

POT1 p.Val391Phe (c.1171G>T) is associated with tumor predisposition syndrome 3 (ClinVar).

How common is POT1 p.Val391Phe (c.1171G>T) in the general population?

POT1 p.Val391Phe (c.1171G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about POT1 p.Val391Phe (c.1171G>T)?

AlphaMissense predicts likely benign (score 0.2665) — an in-silico prediction, not a clinical call.

POT1 p.Val391Phe

c.1171G>T · rs2116462199 · VCV2784751

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2665 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

tumor predisposition syndrome 3

Computational evidence

Protein change
AlphaMissense	0.2665	likely benign
REVEL	0.319	indeterminate
SaProt	LLR -6.54	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP 1.8, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 29 kb · p 0.48 · regional, not allelic
Overall
CADD	25.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: POT1
Protein: p.Val391Phe
Coding: c.1171G>T
MANE Select: NM_015450
dbSNP: rs2116462199
Type: single nucleotide variant
Location: chr7:124841171 (GRCh38)
Gene constraint: LOEUF 0.871 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 87.63 · 14 PDB
Residue 391: 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

Similar variants

POT1 p.Val391Ala Uncertain significance ★★ ⚠ same residue
POT1 p.Val391Ile Uncertain significance ★★ ⚠ same residue
POT1 p.Val391Gly 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

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-val391phe (accessed [today's date]).

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