Is AMPD2 p.Arg270fs (c.808del) pathogenic?

AMPD2 p.Arg270fs (c.808del) is classified Pathogenic in AMPD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-12). Absent from gnomAD; Associated with spastic ataxia.

What condition is associated with AMPD2 p.Arg270fs (c.808del)?

AMPD2 p.Arg270fs (c.808del) is associated with spastic ataxia (ClinVar).

How common is AMPD2 p.Arg270fs (c.808del) in the general population?

AMPD2 p.Arg270fs (c.808del) is absent from gnomAD (gnomAD).

AMPD2 p.Arg270fs

c.808del · rs2101160657 · VCV1027468

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

spastic ataxia

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 8 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.1	GERP 0.75, 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.Arg270fs
Coding: c.808del
MANE Select: NM_001368809
dbSNP: rs2101160657
Type: Deletion
Location: chr1:109627264 (GRCh38)
Gene constraint: LOEUF 0.705 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.28 · 5 PDB
Residue 270: a β-strand

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

Disease context

spastic ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AMPD2 p.Arg270Cys Uncertain significance ★★ ⚠ same residue
AMPD2 p.Arg270His Uncertain significance ★★ ⚠ same residue
AMPD2 p.Gly35fs Pathogenic/Likely pathogenic ★★ same type
AMPD2 p.Leu216fs Pathogenic/Likely pathogenic ★★ same type
AMPD2 c.1408-3_1418del Likely pathogenic ★ same type
AMPD2 p.Ala89fs Pathogenic ★ same type
AMPD2 p.Arg45fs Pathogenic ★ same type
AMPD2 p.Gln101fs Likely pathogenic ★ same type

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-arg270fs (accessed [today's date]).

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