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NM_022166.4(XYLT1):c.1765-8G>A AND Desbuquois dysplasia 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 17, 2022
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:
RCV002812005.2

Allele description

NM_022166.4(XYLT1):c.1765-8G>A

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.1765-8G>A
HGVS:
  • NC_000016.10:g.17134743C>T
  • NG_015843.2:g.341139G>A
  • NM_022166.4:c.1765-8G>AMANE SELECT
  • NC_000016.9:g.17228600C>T
Molecular consequence:
  • NM_022166.4:c.1765-8G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Desbuquois dysplasia 1 (DBQD1)
Synonyms:
MICROMELIC DWARFISM WITH VERTEBRAL AND METAPHYSEAL ABNORMALITIES AND ADVANCED CARPOTARSAL OSSIFICATION; DESBUQUOIS DYSPLASIA 1, KIM VARIANT
Identifiers:
MONDO: MONDO:0009629; MedGen: C4012146; Orphanet: 1425; OMIM: 251450

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003211195Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 17, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003211195.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with XYLT1-related conditions. This variant is present in population databases (rs778442932, gnomAD 0.006%). This sequence change falls in intron 8 of the XYLT1 gene. It does not directly change the encoded amino acid sequence of the XYLT1 protein.

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

Last Updated: Apr 6, 2024