SLC10A2 p.Pro142=
c.426G>T · rs157381 · VCV2784091
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.6 | GERP -3.8 |
| Overall | ||
| CADD | 0.449 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,056 alleles
Filtering AF
0.00111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0009%
Overall
0.00143%
23/1,613,842 alleles · ultra-rare
exomes 21/1,461,606 · genomes 2/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,056 |
| South Asian | 0.0022% | 45,531 |
| European (non-Finnish) | 0.0017% | 58,991 |
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.Pro142=
- Coding
- c.426G>T
- MANE Select
- NM_000452
- dbSNP
- rs157381
- Type
- single nucleotide variant
- Location
- chr13:103058334 (GRCh38)
- Gene constraint
- LOEUF 1.464 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88
Similar variants
- SLC10A2 p.Pro142Leu Conflicting classifications of pathogenicity ★ ⚠ 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-pro142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown