SLIT3 p.Pro935=
c.2805T>C · rs764682671 · VCV2656054
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -13 | GERP -4.2 |
| Overall | ||
| CADD | 0.022 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000558%
9/1,614,072 alleles · ultra-rare
exomes 6/1,461,870 · genomes 3/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00267% | 37,463 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| European (non-Finnish) | 0.000424% | 236,007 |
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.Pro935=
- Coding
- c.2805T>C
- MANE Select
- NM_003062
- dbSNP
- rs764682671
- Type
- single nucleotide variant
- Location
- chr5:168708015 (GRCh38)
- Structure
- AlphaFold pLDDT 80.28
- Residue 935
- the egf-like 1 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-pro935 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown