NM_000379.4(XDH):c.3847C>T (p.Arg1283Ter) AND Xanthinuria type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 27, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001387749.7

Allele description [Variation Report for NM_000379.4(XDH):c.3847C>T (p.Arg1283Ter)]

NM_000379.4(XDH):c.3847C>T (p.Arg1283Ter)

Gene:

XDH:xanthine dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.1

Genomic location:

Preferred name:

NM_000379.4(XDH):c.3847C>T (p.Arg1283Ter)

HGVS:

NC_000002.12:g.31337745G>A
NG_008871.2:g.82001C>T
NM_000379.4:c.3847C>TMANE SELECT
NP_000370.2:p.Arg1283Ter
NC_000002.11:g.31560611G>A
NG_008871.1:g.82001C>T
NM_000379.3:c.3847C>T

Protein change:

R1283*

Links:

dbSNP: rs751921838

NCBI 1000 Genomes Browser:

rs751921838

Molecular consequence:

NM_000379.4:c.3847C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Xanthinuria type II
Synonyms:: Xanthinuria type 2; Xanthine dehydrogenase and aldehyde oxidase combined deficiency of; XDH and AOX dual deficiency
Identifiers:: MONDO: MONDO:0011346; MedGen: C1863688; Orphanet: 3467; OMIM: 603592

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001588459	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 27, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26110747, 9153281, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001588459

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 27, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Xanthinuria type I with a novel mutation of xanthine dehydrogenase.

Tanaka K, Kanazawa I, Yamasaki H, Hasegawa H, Ichida K, Sugimoto T.

Am J Med Sci. 2015 Aug;350(2):155-6. doi: 10.1097/MAJ.0000000000000498. No abstract available.

PubMed [citation]

PMID:: 26110747

Identification of two mutations in human xanthine dehydrogenase gene responsible for classical type I xanthinuria.

Ichida K, Amaya Y, Kamatani N, Nishino T, Hosoya T, Sakai O.

J Clin Invest. 1997 May 15;99(10):2391-7.

PubMed [citation]

PMID:: 9153281
PMCID:: PMC508078

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001588459.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 335758). This premature translational stop signal has been observed in individual(s) with xanthinuria type Œô (PMID: 26110747). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Arg1283*) in the XDH gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in XDH are known to be pathogenic (PMID: 9153281).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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