XYLT2 p.Pro737=
c.2211G>A · rs146573350 · VCV2179586
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0386%, 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 -3.4 | GERP -3.4 |
| Overall | ||
| CADD | 10.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0386%
African / African-American · 29/75,070 alleles
Filtering AF
0.0276%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0238%
Overall
0.00304%
49/1,614,178 alleles · ultra-rare
exomes 25/1,461,818 · genomes 24/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0386% | 2,589 |
| Admixed American | 0.0117% | 8,576 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| South Asian | 0.0011% | 91,082 |
| European (non-Finnish) | 0.000678% | 147,504 |
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.Pro737=
- Coding
- c.2211G>A
- MANE Select
- NM_022167
- dbSNP
- rs146573350
- Type
- single nucleotide variant
- Location
- chr17:50358476 (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-pro737 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown