SLC10A2 p.Ser15=
c.45T>C · rs374581163 · VCV502058
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0356%, eas)
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 -2.3 | GERP -3.5 |
| Overall | ||
| CADD | 0.384 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0356%
East Asian · 16/44,888 alleles
Filtering AF
0.0223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00124%
20/1,613,796 alleles · ultra-rare
exomes 17/1,461,564 · genomes 3/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0356% | 2,805 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
| European (non-Finnish) | 8.48e-05% | 1,179,834 |
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
- SLC10A2
- Protein
- p.Ser15=
- Coding
- c.45T>C
- MANE Select
- NM_000452
- dbSNP
- rs374581163
- Type
- single nucleotide variant
- Location
- chr13:103066205 (GRCh38)
- Gene constraint
- LOEUF 1.464 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88
Similar variants
- SLC10A2 p.Ser15Pro Uncertain significance ★★ ⚠ same residue
- SLC10A2 p.Ala111Val Uncertain significance ★★ ⚠ same type
- SLC10A2 p.Ala116Val Uncertain significance ★★ ⚠ same type
- SLC10A2 p.Ala202Ser Uncertain significance ★★ ⚠ same type
- SLC10A2 p.Ala202Thr Uncertain significance ★★ ⚠ same type
- SLC10A2 p.Ala302Thr Uncertain significance ★★ ⚠ same type
- SLC10A2 p.Ala43Val Uncertain significance ★★ same type
- SLC10A2 p.Arg246Thr 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/slc10a2-p-ser15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown