SLC2A10 p.Pro378=
c.1134C>T · rs892020307 · VCV1611034
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -4.3 | GERP -3.7 |
| Overall | ||
| CADD | 0.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,890 alleles
Overall
0.000137%
2/1,461,876 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,890 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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.Pro378=
- Coding
- c.1134C>T
- MANE Select
- NM_030777
- dbSNP
- rs892020307
- Type
- single nucleotide variant
- Location
- chr20:46726170 (GRCh38)
- Gene constraint
- LOEUF 1.087 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.78
- Residue 378
- the 'disordered' region
Similar variants
- SLC2A10 p.Pro378Ala Uncertain significance ★ ⚠ same residue
- 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
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-pro378 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown