LGI4 p.Asp438=
c.1314C>T · rs779516643 · VCV3034818
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0138%, eas)
Conditions
1
LGI4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.157 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -4.1 |
| Overall | ||
| CADD | 2.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0138%
East Asian · 6/43,594 alleles
Filtering AF
0.00593%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00403%
Overall
0.00147%
23/1,564,486 alleles · ultra-rare
exomes 22/1,412,336 · genomes 1/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0138% | 7,266 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,296 |
| Admixed American | 0.00185% | 54,010 |
| African / African-American | 0.00134% | 74,388 |
| South Asian | 0.00119% | 84,292 |
| European (non-Finnish) | 0.00104% | 96,051 |
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.Asp438=
- Coding
- c.1314C>T
- MANE Select
- NM_139284
- dbSNP
- rs779516643
- Type
- single nucleotide variant
- Location
- chr19:35125493 (GRCh38)
- Gene constraint
- LOEUF 1.255 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.80
- Residue 438
- a UniProt-annotated variant site (in amc1)
Disease context
LGI4-related disorder
Similar variants
- LGI4 p.Asp438Val Uncertain significance ★★ ⚠ 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.Val48= Likely benign same condition
- LGI4 p.Ser279fs Likely pathogenic ★★ same condition
- LGI4 p.Leu11del Likely benign same condition
- LGI4 p.Arg165Cys 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/lgi4-p-asp438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown