Is PLIN1 p.Arg275= (c.825G>T) pathogenic?

PLIN1 p.Arg275= (c.825G>T) is classified Likely benign in PLIN1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-26). Ultra-rare (popmax 0.0115%, amr); Associated with PLIN1-related disorder.

What condition is associated with PLIN1 p.Arg275= (c.825G>T)?

PLIN1 p.Arg275= (c.825G>T) is associated with PLIN1-related disorder (ClinVar).

How common is PLIN1 p.Arg275= (c.825G>T) in the general population?

PLIN1 p.Arg275= (c.825G>T) is ultra-rare (popmax 0.0115%, amr) (gnomAD).

PLIN1 p.Arg275=

c.825G>T · rs747053862 · VCV3053643

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0115%, amr)

Conditions

PLIN1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.093	GERP -3.2
Overall
CADD	4.886	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0115% Admixed American · 6/52,016 alleles

Filtering AF 0.00493% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00341%

Overall 0.000383% 6/1,567,750 alleles · ultra-rare exomes 4/1,415,516 · genomes 2/152,234 · 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: PLIN1
Protein: p.Arg275=
Coding: c.825G>T
MANE Select: NM_002666
dbSNP: rs747053862
Type: single nucleotide variant
Location: chr15:89667740 (GRCh38)
Gene constraint: LOEUF 1.201 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 54.52

Full PLIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PLIN1-related disorder

Similar variants

PLIN1 p.Arg275Gln Uncertain significance ★ ⚠ same residue
PLIN1 p.Arg275Gly Uncertain significance ★ ⚠ same residue
PLIN1 p.Arg275Trp Uncertain significance ★ ⚠ same residue
PLIN1 p.Glu151Lys Uncertain significance ★★ ⚠ same condition
PLIN1 p.Arg329Ter Uncertain significance same condition
PLIN1 p.Cys150Trp Uncertain significance ⚠ same condition
PLIN1 c.-5C>T Likely benign same condition
PLIN1 p.Arg379Ter 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/plin1-p-arg275 (accessed [today's date]).

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