Is PLOD3 p.Leu289fs (c.865del) pathogenic?

PLOD3 p.Leu289fs (c.865del) is classified Pathogenic in PLOD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-25). Absent from gnomAD.

How common is PLOD3 p.Leu289fs (c.865del) in the general population?

PLOD3 p.Leu289fs (c.865del) is absent from gnomAD (gnomAD).

PLOD3 p.Leu289fs

c.865del · rs2535171366 · VCV2693153

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 8 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.3	GERP 3.8, 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: PLOD3
Protein: p.Leu289fs
Coding: c.865del
MANE Select: NM_001084
dbSNP: rs2535171366
Type: Deletion
Location: chr7:101212856 (GRCh38)
Gene constraint: LOEUF 0.925 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 91.80 · 18 PDB
Residue 289: the 'required for glycosyltransferase activity' region

Full PLOD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PLOD3 p.Leu289Phe Uncertain significance ★ ⚠ same residue
PLOD3 c.183_201+9del Likely pathogenic ★ same type
PLOD3 p.Glu660fs Pathogenic ★ same type
PLOD3 p.Pro20fs Pathogenic ★ same type
PLOD3 c.339-11_339-3del Uncertain significance ★ same type
PLOD3 p.Leu722fs Uncertain significance ★ same type
PLOD3 c.1005+16del Likely benign ★ same type
PLOD3 c.1006-3del Likely benign ★ 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/plod3-p-leu289fs (accessed [today's date]).

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