Is LRAT p.Arg55fs (c.163del) pathogenic?

LRAT p.Arg55fs (c.163del) is classified Pathogenic in LRAT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-15). Absent from gnomAD.

How common is LRAT p.Arg55fs (c.163del) in the general population?

LRAT p.Arg55fs (c.163del) is absent from gnomAD (gnomAD).

LRAT p.Arg55fs

c.163del · rs2529972387 · VCV2858521

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

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 2 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP -0.9, 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: LRAT
Protein: p.Arg55fs
Coding: c.163del
MANE Select: NM_004744
dbSNP: rs2529972387
Type: Deletion
Location: chr4:154744486 (GRCh38)
Gene constraint: LOEUF 1.214 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.69
Residue 55: the lrat domain

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

Similar variants

LRAT p.Arg55Gly Pathogenic/Likely pathogenic ★★ same residue
LRAT p.Arg55Trp Pathogenic ★★ same residue
LRAT p.Arg55Gln Uncertain significance ★ ⚠ same residue
LRAT p.Arg55= Likely benign ★ same residue
LRAT p.Arg36fs Pathogenic/Likely pathogenic ★★ same type
LRAT p.Asp33fs Pathogenic/Likely pathogenic ★★ same type
LRAT p.Lys134fs Pathogenic/Likely pathogenic ★★ same type
LRAT p.Met5fs 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/lrat-p-arg55fs (accessed [today's date]).

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