PLOD1 p.Arg111=
c.331C>A · rs772221158 · VCV669058
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000678%, nfe)
Conditions
1
Ehlers-Danlos syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.53 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 21.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000678%
European (non-Finnish) · 8/1,180,024 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000496%
8/1,614,146 alleles · very rare
exomes 8/1,461,840 · genomes 0/152,306 · joint denominator
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
- PLOD1
- Protein
- p.Arg111=
- Coding
- c.331C>A
- MANE Select
- NM_000302
- dbSNP
- rs772221158
- Type
- single nucleotide variant
- Location
- chr1:11950385 (GRCh38)
- Gene constraint
- LOEUF 0.938 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.04
Similar variants
- PLOD1 p.Arg111Gln Uncertain significance ★★ ⚠ same residue
- PLOD1 p.Arg111Trp Uncertain significance ★★ ⚠ same residue
- PLOD1 p.Arg319Ter Pathogenic ★★ same condition
- PLOD1 p.Gln636Ter Pathogenic/Likely pathogenic ★★ same condition
- PLOD1 p.Tyr511Ter Pathogenic ★★ same condition
- PLOD1 p.Arg259Cys Uncertain significance ★★ ⚠ same condition
- PLOD1 p.Arg42His Uncertain significance ★★ ⚠ same condition
- PLOD1 p.Gln119Lys Uncertain significance ★★ ⚠ same condition
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/plod1-p-arg111 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown