SLC35A2 p.Pro322=
c.966A>G · rs373788556 · VCV810586
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000671%, nfe)
Conditions
2
Inborn genetic diseases
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 -7.8 | GERP -1.7 |
| Overall | ||
| CADD | 1.969 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000671%
European (non-Finnish) · 6/894,498 alleles
Filtering AF
0.000241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000496%
6/1,208,841 alleles · very rare
exomes 5/1,097,191 · genomes 1/111,650 · 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
- SLC35A2
- Protein
- p.Pro322=
- Coding
- c.966A>G
- MANE Select
- NM_005660
- dbSNP
- rs373788556
- Type
- single nucleotide variant
- Location
- chrX:48904943 (GRCh38)
- Structure
- AlphaFold pLDDT 80.59
- Residue 322
- 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-pro322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown