LFNG p.Ser169=
c.507G>A · rs780015098 · VCV593622
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00271%, nfe)
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 -12 | GERP -3.1 |
| Overall | ||
| CADD | 0.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00271%
European (non-Finnish) · 32/1,179,902 alleles
Filtering AF
0.00196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00168%
Overall
0.00211%
34/1,612,784 alleles · very rare
exomes 31/1,460,540 · genomes 3/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00271% | 36,872 |
| East Asian | 0.00223% | 44,892 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,456 |
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
- LFNG
- Protein
- p.Ser169=
- Coding
- c.507G>A
- MANE Select
- NM_001040167
- dbSNP
- rs780015098
- Type
- single nucleotide variant
- Location
- chr7:2525244 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.66
Similar variants
- LFNG p.Ser169Leu Uncertain significance ★ ⚠ same residue
- LFNG p.Ser169Pro Uncertain significance ★ ⚠ same residue
- LFNG p.Thr145Met Likely pathogenic ★★ same type
- LFNG c.482-3C>T Uncertain significance ★★ same type
- LFNG p.Ala95Val Uncertain significance ★★ ⚠ same type
- LFNG p.Ala99Thr Uncertain significance ★★ ⚠ same type
- LFNG p.Arg187Cys Uncertain significance ★★ ⚠ same type
- LFNG p.Arg239Trp 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/lfng-p-ser169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown