XPR1 p.Pro307=
c.921G>A · rs151270778 · VCV718143
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.263%, nfe)
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 -0.57 | GERP -3.4 |
| Overall | ||
| CADD | 4.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.263%
European (non-Finnish) · 3,099/1,179,932 alleles
Filtering AF
0.255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.252%
Overall
0.206%
3,331/1,613,698 alleles · rare
exomes 3,157/1,461,516 · genomes 174/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.263% | 381 |
| Remaining individualsnot grpmax-eligible | 0.208% | 481 |
| Admixed American | 0.065% | 1,537 |
| Finnishnot grpmax-eligible | 0.0531% | 1,882 |
| African / African-American | 0.0387% | 2,586 |
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
- XPR1
- Protein
- p.Pro307=
- Coding
- c.921G>A
- MANE Select
- NM_004736
- dbSNP
- rs151270778
- Type
- single nucleotide variant
- Location
- chr1:180824910 (GRCh38)
- Gene constraint
- LOEUF 0.43 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.31 · 51 PDB
- Residue 307
- a β-strand
Similar variants
- XPR1 p.Ala254= Uncertain significance ★★ same type
- XPR1 p.Ala572Val Uncertain significance ★★ ⚠ same type
- XPR1 p.Arg110Cys Uncertain significance ★★ ⚠ same type
- XPR1 p.Arg176Ter Uncertain significance ★★ same type
- XPR1 p.Arg604Gln Uncertain significance ★★ ⚠ same type
- XPR1 p.Arg653Gln Uncertain significance ★★ ⚠ same type
- XPR1 p.Arg655Gly Uncertain significance ★★ ⚠ same type
- XPR1 p.Arg659Gln 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/xpr1-p-pro307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown