SLC2A10 p.Val487=
c.1461C>T · rs1555888585 · VCV515559
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 1.2 | GERP -0.15, phastCons 1 |
| Overall | ||
| CADD | 7.187 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SLC2A10
- Protein
- p.Val487=
- Coding
- c.1461C>T
- MANE Select
- NM_030777
- dbSNP
- rs1555888585
- Type
- single nucleotide variant
- Location
- chr20:46729402 (GRCh38)
- Gene constraint
- LOEUF 1.087 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.78
Similar variants
- SLC2A10 c.1411+2T>A Pathogenic/Likely pathogenic ★★ same type
- SLC2A10 p.Arg105Cys Pathogenic/Likely pathogenic ★★ same type
- SLC2A10 p.Arg132Trp Pathogenic/Likely pathogenic ★★ same type
- SLC2A10 p.Arg229Ter Pathogenic ★★ same type
- SLC2A10 p.Arg231Gln Pathogenic ★★ same type
- SLC2A10 p.Arg231Trp Pathogenic/Likely pathogenic ★★ same type
- SLC2A10 p.Arg444Ter Pathogenic/Likely pathogenic ★★ same type
- SLC2A10 p.Gln243Lys Likely pathogenic ★★ 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/slc2a10-p-val487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown