PLOD1 p.Val104=
c.312G>C · rs1645690488 · VCV2898764
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, afr)
Conditions
1
Ehlers-Danlos syndrome, kyphoscoliotic type 1
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 2.5 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 6.646 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
African / African-American · 5/74,948 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00031%
5/1,614,004 alleles · very rare
exomes 4/1,461,800 · genomes 1/152,204 · 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.Val104=
- Coding
- c.312G>C
- MANE Select
- NM_000302
- dbSNP
- rs1645690488
- Type
- single nucleotide variant
- Location
- chr1:11950366 (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.Val104Met Uncertain significance ★★ ⚠ same residue
- PLOD1 c.1097+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PLOD1 c.1202+2T>C Likely pathogenic ★★ same condition
- PLOD1 c.1470+2T>C Pathogenic/Likely pathogenic ★★ same condition
- PLOD1 c.1471-2A>G Likely pathogenic ★★ same condition
- PLOD1 c.1651-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PLOD1 c.168+1G>T Likely pathogenic ★★ same condition
- PLOD1 c.1903-2A>G Likely pathogenic ★★ 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-val104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown