Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.275%, 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 -0.008 | GERP -4.2, phastCons 0.82 |
| Overall | ||
| CADD | 11.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.275%
African / African-American · 206/75,018 alleles
Filtering AF
0.244%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.232%
Overall
0.018%
290/1,614,140 alleles · rare
exomes 177/1,461,882 · genomes 113/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.275% | 364 |
| South Asian | 0.0626% | 1,598 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Admixed American | 0.015% | 6,669 |
| East Asian | 0.00223% | 44,886 |
| European (non-Finnish) | 0.000424% | 236,008 |
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
- SLC18A2
- Protein
- p.Ser85=
- Coding
- c.255G>A
- MANE Select
- NM_003054
- dbSNP
- rs363388
- Type
- single nucleotide variant
- Location
- chr10:117244104 (GRCh38)
- Gene constraint
- LOEUF 0.68 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.27 · 32 PDB
Similar variants
- SLC18A2 p.Pro387Leu Pathogenic/Likely pathogenic ★★ same type
- SLC18A2 c.834+6C>T Uncertain significance ★★ same type
- SLC18A2 p.Ala164Val Uncertain significance ★★ ⚠ same type
- SLC18A2 p.Ala425Val Uncertain significance ★★ ⚠ same type
- SLC18A2 p.Arg17Cys Uncertain significance ★★ ⚠ same type
- SLC18A2 p.Gly448Glu Uncertain significance ★★ ⚠ same type
- SLC18A2 p.Ile339Val Uncertain significance ★★ ⚠ same type
- SLC18A2 p.Leu260Val Uncertain significance ★★ ⚠ 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/slc18a2-p-ser85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown