SLIT3 p.Ser1289=
c.3867T>C · rs292486 · VCV1242920
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor loss, 13 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.541 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,801/44,806 alleles
Filtering AF
99.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.9%
Overall
96.8%
1,560,952/1,612,538 alleles · common
exomes 1,412,217/1,460,192 · genomes 148,735/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| African / African-American | 99.4% | 1 |
| South Asian | 99% | 1 |
| Amishnot grpmax-eligible | 98.9% | 1 |
| Admixed American | 98.3% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 98.1% | 1 |
| Finnishnot grpmax-eligible | 97.3% | 1 |
| Remaining individualsnot grpmax-eligible | 97.1% | 1 |
| Middle Eastern | 96.6% | 1 |
| European (non-Finnish) | 96.2% | 1 |
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
- SLIT3
- Protein
- p.Ser1289=
- Coding
- c.3867T>C
- MANE Select
- NM_003062
- dbSNP
- rs292486
- Type
- single nucleotide variant
- Location
- chr5:168671458 (GRCh38)
- Structure
- AlphaFold pLDDT 80.28
- Residue 1289
- the laminin g-like domain
Similar variants
- SLIT3 p.Arg682Gln Uncertain significance ★★ ⚠ same type
- SLIT3 p.Gly1518Ser Uncertain significance ★★ ⚠ same type
- SLIT3 p.Lys1348Asn Uncertain significance ★★ ⚠ same type
- SLIT3 p.Met798Thr Uncertain significance ★★ ⚠ same type
- SLIT3 p.Pro1122Gln Uncertain significance ★★ ⚠ same type
- SLIT3 p.Thr535Asn Uncertain significance ★★ ⚠ same type
- SLIT1 c.2970-7C>T Benign ★★ same type
- SLIT1 p.Ala437= Benign ★★ 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/slit3-p-ser1289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown