Is AMOT p.Met410Val (c.1228A>G) pathogenic?

AMOT p.Met410Val (c.1228A>G) is classified Uncertain significance in AMOT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-31). AlphaMissense: likely benign (0.1203); Very rare (popmax 0.00877%, afr).

How common is AMOT p.Met410Val (c.1228A>G) in the general population?

AMOT p.Met410Val (c.1228A>G) is very rare (popmax 0.00877%, afr) (gnomAD).

What do computational predictors say about AMOT p.Met410Val (c.1228A>G)?

AlphaMissense predicts likely benign (score 0.1203) — an in-silico prediction, not a clinical call.

AMOT p.Met410Val

c.1228A>G · rs377126903 · VCV2309957

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1203 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00877%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1203	likely benign
REVEL	0.178	moderately benign-leaning
SaProt	LLR -5.14	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 5	GERP 2.1, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 18 kb · p 0.45 · regional, not allelic
Overall
CADD	18.34	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 0.00877% African / African-American · 5/56,999 alleles

Filtering AF 0.00339% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00216%

Overall 0.000827% 10/1,209,536 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00877%	11,400
South Asian	0.00176%	56,716
European (non-Finnish)	0.000447%	223,797

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.Met410Val
Coding: c.1228A>G
MANE Select: NM_001113490
dbSNP: rs377126903
Type: single nucleotide variant
Location: chrX:112815522 (GRCh38)
Structure: AlphaFold pLDDT 58.16 · 18 PDB
Residue 410: the 'disordered' region; 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.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
AMOT p.Ala460Gly 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-met410val (accessed [today's date]).

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