PLOD2 p.Asn548=
c.1644C>T · rs150609339 · VCV497279
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.719%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 3.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.719%
African / African-American · 533/74,086 alleles
Filtering AF
0.669%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.649%
Overall
0.0378%
597/1,578,482 alleles · rare
exomes 266/1,426,710 · genomes 331/151,772 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.719% | 139 |
| Admixed American | 0.0471% | 2,124 |
| Remaining individualsnot grpmax-eligible | 0.0408% | 2,449 |
| Middle Eastern | 0.0335% | 2,985 |
| European (non-Finnish) | 0.000783% | 127,707 |
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
- PLOD2
- Protein
- p.Asn548=
- Coding
- c.1644C>T
- MANE Select
- NM_182943
- dbSNP
- rs150609339
- Type
- single nucleotide variant
- Location
- chr3:146076815 (GRCh38)
- Gene constraint
- LOEUF 1.209 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.63
- Residue 548
- a UniProt-annotated variant site (in brks2; likely pathogenic)
Similar variants
- PLOD2 c.1500+1G>T Pathogenic/Likely pathogenic ★★ same type
- PLOD2 p.Arg440Ter Pathogenic/Likely pathogenic ★★ same type
- PLOD2 p.Arg473Ter Pathogenic ★★ same type
- PLOD2 p.Arg495Ter Pathogenic/Likely pathogenic ★★ same type
- PLOD2 p.Arg680Ter Pathogenic/Likely pathogenic ★★ same type
- PLOD2 c.1232+5T>A Uncertain significance ★★ same type
- PLOD2 c.-170C>G Uncertain significance ★★ same type
- PLOD2 p.Ala415Val 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/plod2-p-asn548 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown