Is XDH p.Val16= (c.48G>A) pathogenic?

XDH p.Val16= (c.48G>A) is classified Likely benign in XDH (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-07). Absent from gnomAD v4.1; Associated with xanthinuria type II.

What condition is associated with XDH p.Val16= (c.48G>A)?

XDH p.Val16= (c.48G>A) is associated with xanthinuria type II (ClinVar).

How common is XDH p.Val16= (c.48G>A) in the general population?

XDH p.Val16= (c.48G>A) is absent from gnomAD v4.1 (gnomAD).

How is Hereditary xanthinuria inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

XDH p.Val16=

c.48G>A · rs2148010588 · VCV1556616

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

xanthinuria type II

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.29	acceptor loss · deltas
Constraint at this position
Conservation	phyloP 0.002	GERP -2.5, phastCons 0.77
Overall
CADD	5.94	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: XDH
Protein: p.Val16=
Coding: c.48G>A
MANE Select: NM_003104 · reported on NM_000379
dbSNP: rs2148010588
Type: single nucleotide variant
Location: chr2:31405959 (GRCh38)
Structure: AlphaFold pLDDT 98.06 · 3 PDB
Residue 16: a β-strand

Full XDH gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

xanthinuria type II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary xanthinuria (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

Similar variants

SORD p.Gly16Ala Uncertain significance ★ ⚠ same residue
XDH c.1602+1G>A Likely pathogenic ★★ same condition
XDH c.565-1G>A Likely pathogenic ★★ same condition
XDH p.Arg1283Ter Pathogenic ★★ same condition
XDH p.Arg228Ter Pathogenic/Likely pathogenic ★★ same condition
XDH p.Arg825Ter Pathogenic/Likely pathogenic ★★ same condition
XDH p.Gln251Ter Pathogenic/Likely pathogenic ★★ same condition
XDH p.Lys722Ter Pathogenic ★★ same condition

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-val16 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown