Is AMPD2 p.Gln112fs (c.333del) pathogenic?

AMPD2 p.Gln112fs (c.333del) is classified Pathogenic in AMPD2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-01). Absent from gnomAD; Associated with pontocerebellar hypoplasia type 9.

What condition is associated with AMPD2 p.Gln112fs (c.333del)?

AMPD2 p.Gln112fs (c.333del) is associated with pontocerebellar hypoplasia type 9 (ClinVar).

How common is AMPD2 p.Gln112fs (c.333del) in the general population?

AMPD2 p.Gln112fs (c.333del) is absent from gnomAD (gnomAD).

AMPD2 p.Gln112fs

c.333del · rs1650621772 · VCV810627

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

pontocerebellar hypoplasia type 9

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.63	GERP -1.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AMPD2
Protein: p.Gln112fs
Coding: c.333del
MANE Select: NM_001368809
dbSNP: rs1650621772
Type: Deletion
Location: chr1:109625771 (GRCh38)
Gene constraint: LOEUF 0.705 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.28 · 5 PDB

Full AMPD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pontocerebellar hypoplasia type 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AMPD2 p.Gly35fs Pathogenic/Likely pathogenic ★★ same condition
AMPD2 p.Leu216fs Pathogenic/Likely pathogenic ★★ same condition
AMPD2 c.1408-3_1418del Likely pathogenic ★ same condition
AMPD2 p.Gln101fs Likely pathogenic ★ same condition
AMPD2 p.Lys14fs Pathogenic ★ same condition
AMPD2 p.Pro442fs Likely pathogenic ★ same condition
AMPD2 p.Pro90fs Likely pathogenic ★ same condition
AMPD2 p.Tyr295_Pro296insTer Pathogenic ★ 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/ampd2-p-gln112fs (accessed [today's date]).

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