XYLT2 p.Phe561=
c.1683C>T · rs375655126 · VCV1925323
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00934%, afr)
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 -2.7 | GERP -3.1 |
| Overall | ||
| CADD | 1.926 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00934%
African / African-American · 7/74,916 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00112%
18/1,606,800 alleles · very rare
exomes 13/1,454,682 · genomes 5/152,118 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00934% | 10,702 |
| East Asian | 0.00891% | 11,218 |
| European (non-Finnish) | 0.000593% | 168,524 |
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
- XYLT2
- Protein
- p.Phe561=
- Coding
- c.1683C>T
- MANE Select
- NM_022167
- dbSNP
- rs375655126
- Type
- single nucleotide variant
- Location
- chr17:50356711 (GRCh38)
- Gene constraint
- LOEUF 0.689 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.79
Similar variants
- XYLT2 p.Arg563Cys Likely pathogenic ★★ same type
- XYLT2 p.Ala254Val Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala543Thr Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala570Thr Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala614Val Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala807Val Uncertain significance ★★ ⚠ same type
- XYLT2 p.Arg104Lys Uncertain significance ★★ ⚠ same type
- XYLT2 p.Arg107Gln Uncertain significance ★★ ⚠ same type
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/xylt2-p-phe561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown