Is XDH p.Val671= (c.2013G>A) pathogenic?

XDH p.Val671= (c.2013G>A) is classified Benign in XDH (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-18). Low-frequency (popmax 1.97%, sas); Associated with xanthinuria type II.

What condition is associated with XDH p.Val671= (c.2013G>A)?

XDH p.Val671= (c.2013G>A) is associated with xanthinuria type II, xanthinuria type I (ClinVar).

How common is XDH p.Val671= (c.2013G>A) in the general population?

XDH p.Val671= (c.2013G>A) is low-frequency (popmax 1.97%, sas) (gnomAD).

How is Hereditary xanthinuria inherited?

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

XDH p.Val671=

c.2013G>A · rs200635805 · VCV790816

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.97%, sas)

Conditions

xanthinuria type II

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 2.6	GERP 1.9, phastCons 1
Overall
CADD	11.63	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.97% South Asian · 1,798/91,078 alleles

Filtering AF 1.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.87%

Overall 0.122% 1,971/1,614,184 alleles · low-frequency exomes 1,866/1,461,890 · genomes 105/152,294 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	1.97%	51
Remaining individualsnot grpmax-eligible	0.163%	613
East Asian	0.0847%	1,181
Middle Eastern	0.066%	1,516
African / African-American	0.008%	12,506
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
European (non-Finnish)	0.00186%	53,638

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.Val671=
Coding: c.2013G>A
MANE Select: NM_000379
dbSNP: rs200635805
Type: single nucleotide variant
Location: chr2:31368628 (GRCh38)
Structure: AlphaFold pLDDT 98.06 · 3 PDB

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

Also linked: xanthinuria type I

For Hereditary xanthinuria (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

Similar variants

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.Lys57Ter 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-val671 (accessed [today's date]).

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