SLIT3 p.Cys441=
c.1323C>T · rs140499772 · VCV2656062
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.381%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -5.7 |
| Overall | ||
| CADD | 10.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.381%
European (non-Finnish) · 4,494/1,178,762 alleles
Filtering AF
0.372%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.368%
Overall
0.32%
5,156/1,611,642 alleles · rare
exomes 4,856/1,459,326 · genomes 300/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.381% | 262 |
| Remaining individualsnot grpmax-eligible | 0.321% | 312 |
| Admixed American | 0.219% | 456 |
| Finnishnot grpmax-eligible | 0.214% | 466 |
| South Asian | 0.154% | 648 |
| Middle Eastern | 0.0661% | 1,513 |
| African / African-American | 0.0533% | 1,875 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0272% | 3,678 |
| East Asian | 0.00446% | 22,412 |
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.Cys441=
- Coding
- c.1323C>T
- MANE Select
- NM_003062
- dbSNP
- rs140499772
- Type
- single nucleotide variant
- Location
- chr5:168772917 (GRCh38)
- Structure
- AlphaFold pLDDT 80.28
- Residue 441
- the lrrct 2 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-cys441 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown