SLC35A2 p.Ser352=
c.1056T>C · rs56111636 · VCV589375
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, eas)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.028 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.65 | GERP -2.4 |
| Overall | ||
| CADD | 0.456 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
East Asian · 348/33,754 alleles
Filtering AF
0.942%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.907%
Overall
0.0347%
420/1,210,159 alleles · low-frequency
exomes 376/1,097,784 · genomes 44/112,375 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.03% | 97 |
| South Asian | 0.0933% | 1,071 |
| Remaining individualsnot grpmax-eligible | 0.0399% | 2,505 |
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
- SLC35A2
- Protein
- p.Ser352=
- Coding
- c.1056T>C
- MANE Select
- NM_005660
- dbSNP
- rs56111636
- Type
- single nucleotide variant
- Location
- chrX:48904853 (GRCh38)
- Structure
- AlphaFold pLDDT 80.59
- Residue 352
- a UniProt-annotated variant site (in cdg2m); a UniProt-annotated variant site (in cdg2m; reduced udp-galactose transport in patient fibroblasts)
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-ser352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown