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NM_022166.4(XYLT1):c.1651C>T (p.Arg551Cys) AND Desbuquois dysplasia 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 17, 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:
RCV003225190.2

Allele description [Variation Report for NM_022166.4(XYLT1):c.1651C>T (p.Arg551Cys)]

NM_022166.4(XYLT1):c.1651C>T (p.Arg551Cys)

Genes:
LOC102723692:uncharacterized LOC102723692 [Gene]
XYLT1:xylosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p12.3
Genomic location:
Preferred name:
NM_022166.4(XYLT1):c.1651C>T (p.Arg551Cys)
HGVS:
  • NC_000016.10:g.17138468G>A
  • NG_015843.2:g.337414C>T
  • NM_022166.4:c.1651C>TMANE SELECT
  • NP_071449.1:p.Arg551Cys
  • NC_000016.9:g.17232325G>A
  • NM_022166.3:c.1651C>T
  • NR_135179.1:n.373G>A
Protein change:
R551C
Links:
dbSNP: rs776422861
NCBI 1000 Genomes Browser:
rs776422861
Molecular consequence:
  • NM_022166.4:c.1651C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_135179.1:n.373G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
3

Condition(s)

Name:
Desbuquois dysplasia 2 (DBQD2)
Synonyms:
Baratela-Scott syndrome
Identifiers:
MONDO: MONDO:0014343; MedGen: C4014294; Orphanet: 1425; OMIM: 615777

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003920902Zankl Lab, University of Sydney
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Apr 17, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Zankl Lab, University of Sydney, SCV003920902.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testing PubMed (1)

Description

More than 10 XYLT1 mutations have been reported in the literature in association with Desbuquois dysplasia type 2 including missense, nonsense and splice variants as well as small deletions and insertions. This variant was found in the homozygous state in a patient with typical clinical and radiographic features of Desbuquois dysplasia. The same variant was reported previously in the homozygous state in another patient with typical features of Desbuquois dysplasia (PMID: 27481334). The variant has also been previously found in compound heterozygous state with a nonsense variant c.595C>T (p.Gln199*) in a patient with Desbuquois dysplasia (PMID: 2703014). The variant lies in the catalytic domain of XYLT1. Other missense mutations in the catalytic domain of XYLT1 have been reported in patients with Desbuqouis dysplasia (PMID: 24581741). XYLT1 c.1651C>T, p.(Arg551Cys) is classified as pathogenic based on the association between the gene and the patient’s phenotype, rarity in control populations, in silico predicted pathogenicity, and identification of the variant in 3 individuals with the same phenotype.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Jun 23, 2024