Is PLIN3 p.Leu337Pro (c.1010T>C) pathogenic?

PLIN3 p.Leu337Pro (c.1010T>C) is classified Uncertain significance in PLIN3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-10). AlphaMissense: likely pathogenic (0.9495); Very rare (popmax 0.00743%, nfe).

How common is PLIN3 p.Leu337Pro (c.1010T>C) in the general population?

PLIN3 p.Leu337Pro (c.1010T>C) is very rare (popmax 0.00743%, nfe) (gnomAD).

What do computational predictors say about PLIN3 p.Leu337Pro (c.1010T>C)?

AlphaMissense predicts likely pathogenic (score 0.9495) — an in-silico prediction, not a clinical call.

PLIN3 p.Leu337Pro

c.1010T>C · VCV3420803

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9495 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00743%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9495	likely pathogenic · top 1% in PLIN3
REVEL	0.579	indeterminate
SaProt	LLR -15.78	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.5, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 22 kb · p 0.8 · regional, not allelic
Overall
CADD	28.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00743% European (non-Finnish) · 85/1,143,464 alleles

Filtering AF 0.00615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00566%

Overall 0.00574% 89/1,550,702 alleles · very rare exomes 85/1,398,658 · genomes 4/152,044 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00743%	13,453
Remaining individualsnot grpmax-eligible	0.0067%	14,930

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: PLIN3
Protein: p.Leu337Pro
Coding: c.1010T>C
MANE Select: NM_005817
Type: single nucleotide variant
Location: chr19:4839487 (GRCh38)
Gene constraint: LOEUF 1.213 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.04

Full PLIN3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PLIN3 p.Leu337Arg Uncertain significance ★ ⚠ same residue
PLIN3 p.Lys102= Benign ★★ same type
PLIN3 p.Ala139Thr Uncertain significance ★ ⚠ same type
PLIN3 p.Ala212Val Uncertain significance ★ ⚠ same type
PLIN3 p.Ala215Thr Uncertain significance ★ ⚠ same type
PLIN3 p.Ala371Ser Uncertain significance ★ ⚠ same type
PLIN3 p.Ala397Thr Uncertain significance ★ ⚠ same type
PLIN3 p.Ala397Val Uncertain significance ★ ⚠ 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/plin3-p-leu337pro (accessed [today's date]).

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