LINS1 p.Gln475=
c.1425G>A · VCV3906004
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.52e-05%, 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 0.7 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 1.576 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.52e-05%
European (non-Finnish) · 1/1,174,382 alleles
Overall
6.31e-05%
1/1,585,954 alleles · very rare
exomes 1/1,433,704 · genomes 0/152,250 · 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
- LINS1
- Protein
- p.Gln475=
- Coding
- c.1425G>A
- MANE Select
- NM_001040616
- Type
- single nucleotide variant
- Location
- chr15:100570087 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Similar variants
- LINS1 p.Gln475fs Likely pathogenic ★ same residue
- 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
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-gln475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown