LFNG p.Pro92=
c.276C>T · VCV4895023
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0426%, sas)
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 -0.052 | GERP -1.7, phastCons 0.036 |
| Overall | ||
| CADD | 12.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0426%
South Asian · 25/58,636 alleles
Filtering AF
0.0296%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0253%
Overall
0.00189%
26/1,376,446 alleles · ultra-rare
exomes 18/1,225,458 · genomes 8/150,988 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0426% | 2,345 |
| Remaining individualsnot grpmax-eligible | 0.00196% | 51,084 |
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.Pro92=
- Coding
- c.276C>T
- MANE Select
- NM_001040167
- Type
- single nucleotide variant
- Location
- chr7:2520137 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.66
- Residue 92
- the 'disordered' region
Similar variants
- LFNG p.Pro92Leu 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
- LFNG p.Arg246His 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-pro92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown