LINS1 p.Phe498del
c.1491CTT[1] · rs760318837 · VCV1799647
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00588%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.31 | GERP -5.1, phastCons 0.36 |
| Overall | ||
| CADD | 15.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00588%
Admixed American · 3/51,008 alleles
Filtering AF
0.00156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000833%
Overall
0.000387%
6/1,548,832 alleles · very rare
exomes 5/1,396,750 · genomes 1/152,082 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00588% | 17,003 |
| African / African-American | 0.00138% | 72,604 |
| European (non-Finnish) | 0.000173% | 576,552 |
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.Phe498del
- Coding
- c.1491CTT[1]
- MANE Select
- NM_001040616
- dbSNP
- rs760318837
- Type
- Microsatellite
- Location
- chr15:100570016 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Similar variants
- LINS1 p.Ser674fs Likely pathogenic ★★ same condition
- LINS1 c.1394+4A>G Uncertain significance ★★ same condition
- LINS1 p.Ala338Val Uncertain significance ★★ ⚠ same condition
- LINS1 p.Asn433Ser Uncertain significance ★★ ⚠ same condition
- LINS1 p.Asp630Asn Uncertain significance ★★ ⚠ same condition
- LINS1 p.Ile494Thr Uncertain significance ★★ ⚠ same condition
- LINS1 p.Leu757Ter Uncertain significance ★★ same condition
- LINS1 p.Met449Ile Uncertain significance ★★ ⚠ 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/lins1-p-phe498del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown