SLC17A5 p.Phe474=
c.1422T>C · rs766608932 · VCV1116024
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Salla disease
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 |
|---|---|---|
| Pangolin | Δ0.22 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 4.722 | 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
- SLC17A5
- Protein
- p.Phe474=
- Coding
- c.1422T>C
- MANE Select
- NM_012434
- dbSNP
- rs766608932
- Type
- single nucleotide variant
- Location
- chr6:73595143 (GRCh38)
- Gene constraint
- LOEUF 1.065 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.12 · 7 PDB
- Residue 474
- an α-helix
Disease context
Salla disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Free sialic acid storage disease (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Infancy, Neonatal
- Prevalence
- <1 / 1 000 000 (Worldwide)
Similar variants
- SLC17A5 c.1111+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SLC17A5 c.1111+1G>T Likely pathogenic ★★ same condition
- SLC17A5 c.1259+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SLC17A5 c.1259+2T>C Pathogenic ★★ same condition
- SLC17A5 c.1260-2A>C Pathogenic/Likely pathogenic ★★ same condition
- SLC17A5 c.613+1G>A Likely pathogenic ★★ same condition
- SLC17A5 c.700+2T>C Likely pathogenic ★★ same condition
- SLC17A5 c.819+1G>A 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/slc17a5-p-phe474 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown