PLOD3 p.Arg27=
c.81G>A · rs910064708 · VCV2160020
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0383%, afr)
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 -0.23 | GERP 0.39, phastCons 0.007 |
| Overall | ||
| CADD | 9.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0383%
African / African-American · 27/70,496 alleles
Filtering AF
0.0269%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0232%
Overall
0.00214%
32/1,496,444 alleles · ultra-rare
exomes 14/1,344,304 · genomes 18/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0383% | 2,611 |
| Admixed American | 0.00467% | 21,422 |
| Remaining individualsnot grpmax-eligible | 0.00347% | 28,838 |
| European (non-Finnish) | 8.89e-05% | 1,124,638 |
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.Arg27=
- Coding
- c.81G>A
- MANE Select
- NM_001084
- dbSNP
- rs910064708
- Type
- single nucleotide variant
- Location
- chr7:101217194 (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 27
- the 'required for glycosyltransferase activity' 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-arg27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown