Is AMPD1 c.767+12del pathogenic?

AMPD1 c.767+12del is classified Likely benign in AMPD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-01). Very rare (popmax 0.00446%, eas); Associated with myopathy due to myoadenylate deaminase deficiency.

What condition is associated with AMPD1 c.767+12del?

AMPD1 c.767+12del is associated with myopathy due to myoadenylate deaminase deficiency (ClinVar).

How common is AMPD1 c.767+12del in the general population?

AMPD1 c.767+12del is very rare (popmax 0.00446%, eas) (gnomAD).

AMPD1 c.767+12del

rs777942435 · VCV2901187

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

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
Splice region	donor +12	near-intronic (+12 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.72	GERP -3.2
Non-coding constraint	Z 0.26	1 kb window · o/e 0.98 · regional · uncalibrated

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,854 alleles

Filtering AF 0.000739% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000275% 4/1,453,118 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,427
European (non-Finnish)	0.00017%	586,524

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+12del
MANE Select: NM_000036
dbSNP: rs777942435
Type: Deletion
Location: chr1:114680247 (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 c.382-6del Benign/Likely benign ★★ same condition
AMPD1 p.Phe41fs Likely pathogenic ★ same condition
AMPD1 c.216-2del Uncertain significance ★ same condition
AMPD1 c.35-7_35-4del Conflicting classifications of pathogenicity ★ same condition
AMPD1 c.548-3_548-2del Uncertain significance ★ same condition
AMPD1 c.767+3_767+6del Uncertain significance ★ same condition
AMPD1 p.Gly78fs Uncertain significance ★ same condition
AMPD1 p.Ile135fs 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-12del (accessed [today's date]).

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