SLC10A2 p.Ser334=
c.1002A>G · rs1463297260 · VCV2785159
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, 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 0.14 | GERP -0.96, phastCons 0.11 |
| Overall | ||
| CADD | 2.853 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,988 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00124%
20/1,613,884 alleles · very rare
exomes 17/1,461,672 · genomes 3/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,988 |
| European (non-Finnish) | 0.00161% | 62,101 |
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.Ser334=
- Coding
- c.1002A>G
- MANE Select
- NM_000452
- dbSNP
- rs1463297260
- Type
- single nucleotide variant
- Location
- chr13:103046178 (GRCh38)
- Gene constraint
- LOEUF 1.464 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88
- Residue 334
- the 'disordered' region
Similar variants
- 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
- SLC10A2 p.Arg256Gln 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-ser334 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown