SLC35A2 p.Phe220=
c.660T>C · rs2519646178 · VCV2702819
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
SLC35A2-congenital disorder of glycosylation
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.26 | GERP 0.51, phastCons 0.43 |
| Overall | ||
| CADD | 7.545 | 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
- SLC35A2
- Protein
- p.Phe220=
- Coding
- c.660T>C
- MANE Select
- NM_005660
- dbSNP
- rs2519646178
- Type
- single nucleotide variant
- Location
- chrX:48905249 (GRCh38)
- Structure
- AlphaFold pLDDT 80.59
- Residue 220
- a UniProt-annotated variant site (in cdg2m); a UniProt-annotated variant site (in cdg2m; reduced udp-galactose transport in patient fibroblasts)
Disease context
SLC35A2-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor SLC35A2-CDG (Orphanet):
- Inheritance
- Unknown
- Onset
- Infancy, Neonatal
Similar variants
- SLC35A2 p.Gly282Arg Pathogenic ★★ same condition
- SLC35A2 p.Met1Val Pathogenic/Likely pathogenic ★★ same condition
- SLC35A2 p.Tyr267Cys Likely pathogenic ★★ same condition
- SLC35A2 p.Val331Ile Pathogenic ★★ same condition
- SLC35A2 p.Ala11Ser Uncertain significance ★★ ⚠ same condition
- SLC35A2 p.Ala12Gly Uncertain significance ★★ ⚠ same condition
- SLC35A2 p.Ala328Thr Uncertain significance ★★ ⚠ same condition
- SLC35A2 p.Ala344Ser Uncertain significance ★★ ⚠ 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/slc35a2-p-phe220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown