SLIT3 p.Pro1357=
c.4071A>G · VCV4533506
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.73%, afr)
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 -9.6 | GERP -4.2 |
| Overall | ||
| CADD | 0.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.73%
African / African-American · 548/75,046 alleles
Filtering AF
0.68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.66%
Overall
0.0393%
634/1,613,382 alleles · rare
exomes 327/1,461,088 · genomes 307/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.73% | 137 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,301 |
| Admixed American | 0.0533% | 1,875 |
| Middle Eastern | 0.0332% | 3,011 |
| South Asian | 0.0022% | 45,527 |
| European (non-Finnish) | 0.00017% | 589,939 |
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.Pro1357=
- Coding
- c.4071A>G
- MANE Select
- NM_003062
- Type
- single nucleotide variant
- Location
- chr5:168671254 (GRCh38)
- Structure
- AlphaFold pLDDT 80.28
- Residue 1357
- the egf-like 7 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-pro1357 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown