SLIT3 p.Asp502=
c.1506C>T · rs150725100 · VCV2656059
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.482%, 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 2.5 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 7.957 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.482%
European (non-Finnish) · 5,687/1,179,990 alleles
Filtering AF
0.471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.467%
Overall
0.368%
5,934/1,614,122 alleles · rare
exomes 5,619/1,461,828 · genomes 315/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.482% | 207 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| Remaining individualsnot grpmax-eligible | 0.203% | 492 |
| Admixed American | 0.0866% | 1,154 |
| African / African-American | 0.06% | 1,668 |
| Finnishnot grpmax-eligible | 0.0297% | 3,369 |
| South Asian | 0.0022% | 45,544 |
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.Asp502=
- Coding
- c.1506C>T
- MANE Select
- NM_003062
- dbSNP
- rs150725100
- Type
- single nucleotide variant
- Location
- chr5:168762643 (GRCh38)
- Structure
- AlphaFold pLDDT 80.28
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-asp502 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown