LINS1 p.Glu366Ter
c.1096G>T · rs1131691716 · VCV429992
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 7 |
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -0.15, phastCons 0.013 |
| Overall | ||
| CADD | 36.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- LINS1
- Protein
- p.Glu366Ter
- Coding
- c.1096G>T
- MANE Select
- NM_001040616
- dbSNP
- rs1131691716
- Type
- single nucleotide variant
- Location
- chr15:100573777 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Similar variants
- LINS1 p.Leu393Ter Pathogenic/Likely pathogenic ★★ same type
- LINS1 c.1394+4A>G Uncertain significance ★★ same type
- LINS1 p.Ala338Val Uncertain significance ★★ ⚠ same type
- LINS1 p.Asn433Ser Uncertain significance ★★ ⚠ same type
- LINS1 p.Asp221Asn Uncertain significance ★★ ⚠ same type
- LINS1 p.Asp630Asn Uncertain significance ★★ ⚠ same type
- LINS1 p.Ile494Thr Uncertain significance ★★ ⚠ same type
- LINS1 p.Leu757Ter 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/lins1-p-glu366ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown