Is OAT p.Phe260fs (c.780del) pathogenic?

OAT p.Phe260fs (c.780del) is classified Pathogenic/Likely pathogenic in OAT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-09-08). No gnomAD frequency available for this variant; Associated with OAT-related disorder.

What condition is associated with OAT p.Phe260fs (c.780del)?

OAT p.Phe260fs (c.780del) is associated with OAT-related disorder, ornithine aminotransferase deficiency (ClinVar).

How common is OAT p.Phe260fs (c.780del) in the general population?

OAT p.Phe260fs (c.780del) is no gnomAD frequency available for this variant (gnomAD).

OAT p.Phe260fs

c.780del · rs2134456707 · VCV1072300

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

OAT-related disorder

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 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.1	GERP 2, 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: OAT
Protein: p.Phe260fs
Coding: c.780del
MANE Select: NM_000274
dbSNP: rs2134456707
Type: Deletion
Location: chr10:124403047 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 260: a β-strand

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

Disease context

OAT-related disorder

Also linked: ornithine aminotransferase deficiency

Similar variants

OAT c.881_900+51del Likely pathogenic ★★ same condition
OAT p.Ala61fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.Glu318fs Pathogenic ★★ same condition
OAT p.Gly67fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.His53fs Pathogenic ★★ same condition
OAT p.Leu259fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.Phe172fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.Phe177_Trp178insTer 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/oat-p-phe260fs (accessed [today's date]).

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