Is MTOR p.Phe594fs (c.1782del) pathogenic?

MTOR p.Phe594fs (c.1782del) is classified Uncertain significance in MTOR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-10-11). No gnomAD frequency available for this variant.

How common is MTOR p.Phe594fs (c.1782del) in the general population?

MTOR p.Phe594fs (c.1782del) is no gnomAD frequency available for this variant (gnomAD).

MTOR p.Phe594fs

c.1782del · rs2100909155 · VCV1331592

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 11 of 58
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MTOR
Protein: p.Phe594fs
Coding: c.1782del
MANE Select: NM_004958
dbSNP: rs2100909155
Type: Deletion
Location: chr1:11240307 (GRCh38)
Gene constraint: LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 78.57 · 73 PDB
Residue 594: the 'interaction with nbn' region

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

Similar variants

MTOR c.1413-3_1413-2del Likely benign ★★ same type
MTOR c.162+19del Benign/Likely benign ★★ same type
MTOR c.2779+12del Benign/Likely benign ★★ same type
MTOR p.1830_1833TAAT[1] Benign/Likely benign ★★ same type
MTOR p.Lys1452_Glu1455del Likely pathogenic ★ same type
MTOR c.1116+1del Uncertain significance ★ same type
MTOR c.3286-2del Uncertain significance ★ same type
MTOR c.4999-17_4999-1del Uncertain significance ★ same type

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/mtor-p-phe594fs (accessed [today's date]).

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