LGI4 p.Val48=
c.144C>G · rs1271333075 · VCV3035544
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00249%, nfe)
Conditions
1
LGI4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.62 | GERP -1.6, phastCons 0.95 |
| Overall | ||
| CADD | 5.539 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00249%
European (non-Finnish) · 29/1,166,632 alleles
Filtering AF
0.00174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00151%
Overall
0.00183%
29/1,585,704 alleles · very rare
exomes 29/1,433,346 · genomes 0/152,358 · 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
- LGI4
- Protein
- p.Val48=
- Coding
- c.144C>G
- MANE Select
- NM_139284
- dbSNP
- rs1271333075
- Type
- single nucleotide variant
- Location
- chr19:35134537 (GRCh38)
- Gene constraint
- LOEUF 1.255 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.80
Disease context
LGI4-related disorder
Similar variants
- LGI4 p.Val48Leu Uncertain significance ★ ⚠ same residue
- LGI4 p.Val48Ile Likely benign ★ same residue
- LGI4 c.793+7C>T Likely benign same condition
- LGI4 p.Ala12= Likely benign same condition
- LGI4 p.Ala265= Likely benign same condition
- LGI4 p.Asp438= Likely benign same condition
- LGI4 p.Ser279fs Likely pathogenic ★★ same condition
- LGI4 p.Leu11del Likely benign 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/lgi4-p-val48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown