SLC2A10 p.Ser89=
c.267C>T · rs747559824 · VCV415524
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Conditions
1
arterial tortuosity syndrome
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 1.8 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,030 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000124%
2/1,614,090 alleles · very rare
exomes 2/1,461,758 · genomes 0/152,332 · joint denominator
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
- SLC2A10
- Protein
- p.Ser89=
- Coding
- c.267C>T
- MANE Select
- NM_030777
- dbSNP
- rs747559824
- Type
- single nucleotide variant
- Location
- chr20:46725303 (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 condition
- SLC2A10 p.Arg105Cys Pathogenic/Likely pathogenic ★★ same condition
- SLC2A10 p.Arg132Trp Pathogenic/Likely pathogenic ★★ same condition
- SLC2A10 p.Arg229Ter Pathogenic ★★ same condition
- SLC2A10 p.Arg231Gln Pathogenic ★★ same condition
- SLC2A10 p.Arg231Trp Pathogenic/Likely pathogenic ★★ same condition
- SLC2A10 p.Arg444Ter Pathogenic/Likely pathogenic ★★ same condition
- SLC2A10 p.Gln243Lys Likely pathogenic ★★ same condition
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-ser89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown