Is MTOR p.Arg53fs (c.157dup) pathogenic?

MTOR p.Arg53fs (c.157dup) is classified Uncertain significance in MTOR (ClinVar, Single submitter, 1 submitter; last evaluated 2021-02-06). No gnomAD frequency available for this variant.

How common is MTOR p.Arg53fs (c.157dup) in the general population?

MTOR p.Arg53fs (c.157dup) is no gnomAD frequency available for this variant (gnomAD).

MTOR p.Arg53fs

c.157dup · rs2100986052 · VCV1407560

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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 2 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.Arg53fs
Coding: c.157dup
MANE Select: NM_004958
dbSNP: rs2100986052
Type: Duplication
Location: chr1:11259252 (GRCh38)
Gene constraint: LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 78.57 · 73 PDB
Residue 53: the 'interaction with nbn' region

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

Similar variants

MTOR p.Arg53Gln Uncertain significance ★★ ⚠ same residue
MTOR p.Arg53Ter Uncertain significance ★★ same residue
MTOR p.Leu2097fs Uncertain significance ★★ same type
MTOR c.4687-12dup Likely benign ★★ same type
MTOR c.841-18dup Benign/Likely benign ★★ same type
MTOR p.Thr2436_Lys2437insAsn Likely benign ★★ same type
MTOR c.3945-26_4016dup Likely pathogenic ★ same type
MTOR p.Ala1835_Thr1840dup Conflicting classifications of pathogenicity ★ 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-arg53fs (accessed [today's date]).

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