Is AMOT p.Arg549Cys (c.1645C>T) pathogenic?

AMOT p.Arg549Cys (c.1645C>T) is classified Uncertain significance in AMOT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-29). AlphaMissense: likely benign (0.3038); Ultra-rare (popmax 0.057%, amr).

How common is AMOT p.Arg549Cys (c.1645C>T) in the general population?

AMOT p.Arg549Cys (c.1645C>T) is ultra-rare (popmax 0.057%, amr) (gnomAD).

What do computational predictors say about AMOT p.Arg549Cys (c.1645C>T)?

AlphaMissense predicts likely benign (score 0.3038) — an in-silico prediction, not a clinical call.

AMOT p.Arg549Cys

c.1645C>T · VCV4640244

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3038 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.057%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3038	likely benign
REVEL	0.19	benign-leaning
SaProt	LLR -8.18	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP -3.1, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 18 kb · p 0.45 · regional, not allelic
Overall
CADD	22.6	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

Grpmax group 0.057% Admixed American · 26/45,652 alleles

Filtering AF 0.0398% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0342%

Overall 0.00256% 31/1,209,299 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.057%	1,756
Remaining individualsnot grpmax-eligible	0.0042%	23,789
Finnishnot grpmax-eligible	0.00215%	46,483
European (non-Finnish)	0.000223%	447,535

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: AMOT
Protein: p.Arg549Cys
Coding: c.1645C>T
MANE Select: NM_001113490
Type: single nucleotide variant
Location: chrX:112805078 (GRCh38)
Structure: AlphaFold pLDDT 58.16 · 18 PDB
Residue 549: the 'involved in interaction with yap1' region

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

Similar variants

AMOT p.Arg549His Uncertain significance ★ ⚠ same residue
AMOT p.Ala1032Val Benign ★★ same type
AMOT p.Ser316= Benign ★★ same type
AMOT p.Ser538= Benign ★★ same type
AMOT p.Ser780= Benign ★★ same type
AMOT p.Thr899Ala Benign ★★ same type
AMOT p.Gln642His Likely pathogenic ★ ⚠ same type
AMOT p.Ala1023Pro 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/amot-p-arg549cys (accessed [today's date]).

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