Is APTX p.Val259fs (c.776del) pathogenic?

APTX p.Val259fs (c.776del) is classified Pathogenic in APTX (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-06-20). Very rare (popmax 0.00112%, sas); Associated with ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia.

What condition is associated with APTX p.Val259fs (c.776del)?

APTX p.Val259fs (c.776del) is associated with ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia (ClinVar).

How common is APTX p.Val259fs (c.776del) in the general population?

APTX p.Val259fs (c.776del) is very rare (popmax 0.00112%, sas) (gnomAD).

How is Ataxia-oculomotor apraxia type 1 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

APTX p.Val259fs

c.776del · rs1563945076 · VCV635168

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00112%, sas)

Conditions

ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia

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 7 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.17	GERP -2.3, phastCons 0.66

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00112% South Asian · 1/89,398 alleles

Overall 6.3e-05% 1/1,586,970 alleles · very rare exomes 1/1,450,170 · genomes 0/136,800 · joint denominator

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: APTX
Protein: p.Val259fs
Coding: c.776del
MANE Select: NM_001195248
dbSNP: rs1563945076
Type: Deletion
Location: chr9:32974556 (GRCh38)
Gene constraint: LOEUF 0.973 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.52 · 11 PDB
Residue 259: the hit domain

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

Disease context

ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Ataxia-oculomotor apraxia type 1 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

APTX p.Arg199fs Pathogenic/Likely pathogenic ★★ same condition
APTX c.484-25_484-4del Benign ★★ same condition
APTX c.484-25_484-5del Benign/Likely benign ★★ same condition
APTX c.484-25_484-6del Benign ★★ same condition
APTX p.Val259= Likely benign ★★ same residue
APTX c.874+1del Likely pathogenic ★ same condition
APTX p.Leu213fs Pathogenic ★ same condition
APTX p.Lys243fs Likely 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/aptx-p-val259fs (accessed [today's date]).

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