XDH p.Asp674=
c.2022C>T · rs185713366 · VCV3034935
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 2.4 | GERP 0.92, phastCons 1 |
| Overall | ||
| CADD | 7.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,034 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000186%
3/1,614,196 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,017 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
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.Asp674=
- Coding
- c.2022C>T
- MANE Select
- NM_003104 · reported on NM_000379
- dbSNP
- rs185713366
- Type
- single nucleotide variant
- Location
- chr2:31368619 (GRCh38)
- Structure
- AlphaFold pLDDT 98.06 · 3 PDB
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.Thr151= 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-asp674 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown