Is AMPD1 c.767+7G>A pathogenic?

AMPD1 c.767+7G>A is classified Likely benign in AMPD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-23). Very rare (popmax 0.0011%, sas); Associated with myopathy due to myoadenylate deaminase deficiency.

What condition is associated with AMPD1 c.767+7G>A?

AMPD1 c.767+7G>A is associated with myopathy due to myoadenylate deaminase deficiency (ClinVar).

How common is AMPD1 c.767+7G>A in the general population?

AMPD1 c.767+7G>A is very rare (popmax 0.0011%, sas) (gnomAD).

AMPD1 c.767+7G>A

rs774393161 · VCV1656116

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

myopathy due to myoadenylate deaminase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
Splice region	donor +7	near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone
SpliceAI	Δ0.23	donor gain · deltas
Constraint at this position
Conservation	phyloP -1.6	GERP -3.4
Non-coding constraint	Z 0.26	1 kb window · o/e 0.98 · regional · uncalibrated
Overall
CADD	4.657	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,014 alleles

Overall 0.000137% 2/1,460,232 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,014
European (non-Finnish)	8.48e-05%	1,179,357

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
Coding: c.767+7G>A
MANE Select: NM_000036
dbSNP: rs774393161
Type: single nucleotide variant
Location: chr1:114680252 (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-c-767-plus-7g-a (accessed [today's date]).

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