Is AMPD1 p.Met662Ile (c.1986G>A) pathogenic?

AMPD1 p.Met662Ile (c.1986G>A) is classified Uncertain significance in AMPD1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-01-22). AlphaMissense: likely pathogenic (0.8196); Ultra-rare (popmax 0.0493%, nfe); Associated with Inborn genetic diseases.

What condition is associated with AMPD1 p.Met662Ile (c.1986G>A)?

AMPD1 p.Met662Ile (c.1986G>A) is associated with Inborn genetic diseases, myopathy due to myoadenylate deaminase deficiency (ClinVar).

How common is AMPD1 p.Met662Ile (c.1986G>A) in the general population?

AMPD1 p.Met662Ile (c.1986G>A) is ultra-rare (popmax 0.0493%, nfe) (gnomAD).

What do computational predictors say about AMPD1 p.Met662Ile (c.1986G>A)?

AlphaMissense predicts likely pathogenic (score 0.8196) — an in-silico prediction, not a clinical call.

AMPD1 p.Met662Ile

c.1986G>A · rs115092288 · VCV1424886

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8196 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0493%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8196	likely pathogenic
REVEL	0.644	pathogenic-leaning
⇒ AlphaMissense and REVEL both call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.71	unconstrained · MANE · 862 bp · p 0.00064 · regional, not allelic
Overall
CADD	25.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM M695I vs ClinVar M662I) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0493% European (non-Finnish) · 581/1,179,398 alleles

Filtering AF 0.0459% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0446%

Overall 0.0424% 684/1,613,344 alleles · ultra-rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	2.63%	38
Finnishnot grpmax-eligible	0.0531%	1,882
European (non-Finnish)grpmax	0.0493%	2,030
Remaining individualsnot grpmax-eligible	0.0384%	2,604
Admixed American	0.0267%	3,751
African / African-American	0.00533%	18,747
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,592

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: AMPD1
Protein: p.Met662Ile
Coding: c.1986G>A
MANE Select: NM_000036
dbSNP: rs115092288
Type: single nucleotide variant
Location: chr1:114673738 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.84

Full AMPD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: myopathy due to myoadenylate deaminase deficiency

Similar variants

AMPD1 p.Gln653Ter Pathogenic/Likely pathogenic ★★ same condition
AMPD1 c.1388+5G>A Uncertain significance ★★ same condition
AMPD1 c.1974+1G>A Uncertain significance ★★ same condition
AMPD1 c.-42C>T Uncertain significance ★★ ⚠ same condition
AMPD1 p.Ala308Thr Uncertain significance ★★ ⚠ same condition
AMPD1 p.Ala489Thr Uncertain significance ★★ ⚠ same condition
AMPD1 p.Ala578Thr Uncertain significance ★★ ⚠ same condition
AMPD1 p.Ala616Thr Uncertain significance ★★ ⚠ 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/ampd1-p-met662ile (accessed [today's date]).

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