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NM_000379.4(XDH):c.3847C>T (p.Arg1283Ter) AND Hereditary xanthinuria type 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 28, 2017
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:
RCV000333311.5

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:
Hereditary xanthinuria type 1 (XAN1)
Synonyms:
Xanthinuria type 1; XDH deficiency
Identifiers:
MONDO: MONDO:0010209; MedGen: C0268118; Orphanet: 3467; OMIM: 278300

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000430017Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)		Uncertain significance
(Apr 28, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000430017.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The XDH c. 3847C>T (p.Arg1283Ter) variant is a stop-gained variant which has been reported in one study in which it is found in one individual with xanthinuria in a homozygous state (Tanaka et al. 2015). The individual had elevated xanthine levels in the plasma and urine and edema of the right leg. Control data are unavailable for this variant, which is reported at a frequency of 0.00009 in the Latino population of the Exome Aggregation Consortium, but this is based on one allele in a region of good sequence coverage so the variant is presumed to be rare. Due to the potential impact of stop-gained variants and the limited evidence available, the p.Arg1283Ter variant is classified as a variant of unknown significance but suspicious for pathogenicity for xanthinuria. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024