SLC10A2 p.Val8=
c.24G>A · rs1042375031 · VCV720612
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
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 -2.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.184 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,948 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00062%
10/1,611,820 alleles · ultra-rare
exomes 5/1,459,616 · genomes 5/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,991 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,595 |
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.Val8=
- Coding
- c.24G>A
- MANE Select
- NM_000452
- dbSNP
- rs1042375031
- Type
- single nucleotide variant
- Location
- chr13:103066226 (GRCh38)
- Gene constraint
- LOEUF 1.464 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88
Similar variants
- SLC10A2 p.Val8Met 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-val8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown