Is PLOD3 p.Arg657= (c.1971G>A) pathogenic?

PLOD3 p.Arg657= (c.1971G>A) is classified Likely benign in PLOD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-31). No allele count reported in gnomAD v4.1 (AN 1,560,596).

How common is PLOD3 p.Arg657= (c.1971G>A) in the general population?

PLOD3 p.Arg657= (c.1971G>A) is no allele count reported in gnomAD v4.1 (AN 1,560,596) (gnomAD).

PLOD3 p.Arg657=

c.1971G>A · VCV4897205

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,560,596)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.025	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.78	GERP 2.1, phastCons 1
Overall
CADD	5.531	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,560,596). 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.Arg657=
Coding: c.1971G>A
MANE Select: NM_001084
Type: single nucleotide variant
Location: chr7:101206869 (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 657: the fe2og dioxygenase domain; a UniProt-annotated variant site (in bcard; uncertain significance)

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

Similar variants

PLOD3 p.Arg657Gly Uncertain significance ★ ⚠ same residue
PLOD3 p.Arg657Leu Uncertain significance ★ ⚠ same residue
PLOD3 p.Arg657Trp Uncertain significance ★ same residue
PLOD3 c.1359-1G>C Likely pathogenic ★★ same type
PLOD3 p.Arg452Ter Pathogenic ★★ same type
PLOD3 p.Tyr630Ter Pathogenic/Likely pathogenic ★★ same type
PLOD3 c.338+6G>C Uncertain significance ★★ same type
PLOD3 p.Ala371Val 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/plod3-p-arg657 (accessed [today's date]).

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