SLC10A2 p.Pro94=
c.282G>A · rs143884320 · VCV2874503
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0825%, 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 -6.5 | GERP -3.8 |
| Overall | ||
| CADD | 0.118 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0825%
Middle Eastern · 5/6,060 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.00378%
61/1,614,016 alleles · ultra-rare
exomes 42/1,461,826 · genomes 19/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0825% | 1,212 |
| African / African-American | 0.028% | 3,572 |
| Admixed American | 0.0133% | 7,500 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.00153% | 65,554 |
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.Pro94=
- Coding
- c.282G>A
- MANE Select
- NM_000452
- dbSNP
- rs143884320
- Type
- single nucleotide variant
- Location
- chr13:103065968 (GRCh38)
- Gene constraint
- LOEUF 1.464 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88
Similar variants
- SLC10A2 p.Pro94Leu Uncertain significance ★★ ⚠ same residue
- SLC10A2 p.Pro94fs 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
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-pro94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown