PLOD3 p.Ala301=
c.903C>T · rs150312907 · VCV2163905
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.131%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.057 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.48 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.38 | GERP 1.9, phastCons 0.003 |
| Overall | ||
| CADD | 12.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.131%
African / African-American · 98/74,964 alleles
Filtering AF
0.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.102%
Overall
0.00725%
117/1,613,850 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.131% | 765 |
| Admixed American | 0.00834% | 11,996 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,623 |
| East Asian | 0.00446% | 22,436 |
| European (non-Finnish) | 0.000678% | 147,490 |
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.Ala301=
- Coding
- c.903C>T
- MANE Select
- NM_001084
- dbSNP
- rs150312907
- Type
- single nucleotide variant
- Location
- chr7:101212632 (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 301
- the 'accessory region' region; a β-strand
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-ala301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown