PLOD3 p.Ser367=
c.1101C>T · VCV3698146
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0286%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.051 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.87 | GERP 0.47 |
| Overall | ||
| CADD | 5.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0286%
South Asian · 26/91,064 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0171%
Overall
0.00167%
27/1,613,370 alleles · ultra-rare
exomes 24/1,461,184 · genomes 3/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0286% | 3,502 |
| European (non-Finnish) | 8.47e-05% | 1,179,988 |
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
- PLOD3
- Protein
- p.Ser367=
- Coding
- c.1101C>T
- MANE Select
- NM_001084
- Type
- single nucleotide variant
- Location
- chr7:101212279 (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 367
- the 'accessory region' region
Similar variants
- 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
- PLOD3 p.Ala431Thr Uncertain significance ★★ ⚠ same type
- PLOD3 p.Ala59Val Uncertain significance ★★ ⚠ same type
- PLOD3 p.Ala646Val 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-ser367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown