PLOD3 p.Val41=
c.123G>A · rs112321807 · VCV440173
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.4%, sas)
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 0.48 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 12.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.4%
South Asian · 2,187/91,020 alleles
Filtering AF
2.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.28%
Overall
0.474%
7,646/1,612,726 alleles · low-frequency
exomes 7,075/1,460,424 · genomes 571/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.4% | 42 |
| Middle Eastern | 1.78% | 56 |
| Remaining individualsnot grpmax-eligible | 0.557% | 179 |
| Ashkenazi Jewishnot grpmax-eligible | 0.436% | 229 |
| European (non-Finnish) | 0.385% | 260 |
| African / African-American | 0.237% | 421 |
| Admixed American | 0.173% | 577 |
| Finnishnot grpmax-eligible | 0.0656% | 1,524 |
| East Asian | 0.0178% | 5,609 |
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.Val41=
- Coding
- c.123G>A
- MANE Select
- NM_001084
- dbSNP
- rs112321807
- Type
- single nucleotide variant
- Location
- chr7:101216773 (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 41
- the 'required for glycosyltransferase activity' 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-val41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown