Is AMPD1 p.Glu488= (c.1464G>A) pathogenic?

AMPD1 p.Glu488= (c.1464G>A) is classified Benign in AMPD1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-30). Low-frequency (popmax 3.07%, sas); Associated with myopathy due to myoadenylate deaminase deficiency.

What condition is associated with AMPD1 p.Glu488= (c.1464G>A)?

AMPD1 p.Glu488= (c.1464G>A) is associated with myopathy due to myoadenylate deaminase deficiency (ClinVar).

How common is AMPD1 p.Glu488= (c.1464G>A) in the general population?

AMPD1 p.Glu488= (c.1464G>A) is low-frequency (popmax 3.07%, sas) (gnomAD).

AMPD1 p.Glu488=

c.1464G>A · rs80266556 · VCV166682

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.07%, sas)

Conditions

myopathy due to myoadenylate deaminase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.38	GERP -0.66, phastCons 0.99
Overall
CADD	7.551	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.07% South Asian · 2,793/91,084 alleles

Filtering AF 2.97% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.93%

Overall 0.509% 8,219/1,614,086 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	3.07%	33
Middle Eastern	1.83%	55
African / African-American	1.64%	61
Remaining individualsnot grpmax-eligible	0.653%	153
Ashkenazi Jewishnot grpmax-eligible	0.547%	183
Admixed American	0.453%	221
European (non-Finnish)	0.269%	372
Finnishnot grpmax-eligible	0.0844%	1,185
East Asian	0.0446%	2,244

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.Glu488=
Coding: c.1464G>A
MANE Select: NM_000036
dbSNP: rs80266556
Type: single nucleotide variant
Location: chr1:114675928 (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

myopathy due to myoadenylate deaminase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-glu488 (accessed [today's date]).

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