XDH p.Thr151=
c.453A>G · VCV3350207
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
Conditions
1
XDH-related disorder
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 -3.1 | GERP -3.7 |
| Overall | ||
| CADD | 6.444 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,876 alleles · very rare
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
- XDH
- Protein
- p.Thr151=
- Coding
- c.453A>G
- MANE Select
- NM_003104 · reported on NM_000379
- Type
- single nucleotide variant
- Location
- chr2:31397710 (GRCh38)
- Structure
- AlphaFold pLDDT 98.06 · 3 PDB
- Residue 151
- a UniProt-annotated variant site (in hmnr8); an α-helix
Disease context
XDH-related disorder
Similar variants
- XDH p.Arg228Ter Pathogenic/Likely pathogenic ★★ same condition
- XDH p.Gln158Ter Likely pathogenic ★ same condition
- XDH p.Val1180Ala Uncertain significance ⚠ same condition
- XDH c.3775-6G>T Likely benign same condition
- XDH p.Asp674= Likely benign same condition
- XDH p.Pro214fs Pathogenic ★★ same condition
- XDH p.Glu309fs Likely pathogenic ★ same condition
- SORD p.Ala153Asp Pathogenic/Likely pathogenic ★★ 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/xdh-p-thr151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown