NM_022166.4(XYLT1):c.1588-3C>T AND Desbuquois dysplasia 2

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 6, 2020
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000115037.6

Allele description [Variation Report for NM_022166.4(XYLT1):c.1588-3C>T]

NM_022166.4(XYLT1):c.1588-3C>T

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.1588-3C>T

HGVS:

NC_000016.10:g.17138534G>A
NG_015843.2:g.337348C>T
NM_022166.4:c.1588-3C>TMANE SELECT
NC_000016.9:g.17232391G>A
NG_015843.1:g.337348C>T
NM_022166.3:c.1588-3C>T
NR_135179.1:n.439G>A

Nucleotide change:

IVS7, C-T, -3

Links:

OMIM: 608124.0006; dbSNP: rs201818754

NCBI 1000 Genomes Browser:

rs201818754

Molecular consequence:

NM_022166.4:c.1588-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NR_135179.1:n.439G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000148946	OMIM	no assertion criteria provided	Pathogenic (Mar 6, 2014)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV001142462	Reproductive Health Research and Development, BGI Genomics	no assertion criteria provided	Uncertain significance (Jan 6, 2020)	germline	curation

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000148946

OMIM

no assertion criteria provided

Pathogenic
(Mar 6, 2014)

germline

literature only

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

SCV001142462

Reproductive Health Research and Development, BGI Genomics

no assertion criteria provided

Uncertain significance
(Jan 6, 2020)

germline

curation

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

XYLT1 mutations in Desbuquois dysplasia type 2.

Bui C, Huber C, Tuysuz B, Alanay Y, Bole-Feysot C, Leroy JG, Mortier G, Nitschke P, Munnich A, Cormier-Daire V.

Am J Hum Genet. 2014 Mar 6;94(3):405-14. doi: 10.1016/j.ajhg.2014.01.020. Epub 2014 Feb 27.

PubMed [citation]

PMID:: 24581741
PMCID:: PMC3951945

Details of each submission

From OMIM, SCV000148946.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a Turkish patient with Desbuquois dysplasia-2 (DBQD2; 615777), Bui et al. (2014) identified homozygosity for a c.1588-3C-T transition in intron 7 of the XYLT1 gene. His unaffected parents were heterozygous for the mutation, which was not found in 200 control chromosomes.

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

From Reproductive Health Research and Development, BGI Genomics, SCV001142462.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

NG_015843.1(NM_022166.3):c.1588-3C>T in XYLT1 gene has an allele frequency of 0.006 in Ashkenazi Jewish subpopulation in the gnomAD database. 3 homozygous occurrences are observed in the gnomAD database. This variant has been detected in an individual with Desbuquois dysplasia 2 (PMID: 24581741). Benign computational verdict because benign prediction from DANN. The available evidence is currently insufficient to determine the role of this variant in disease. We interpret it as variant of uncertain significance (VUS). ACMG/AMP criteria applied: PP3; PP4.

#	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: Oct 20, 2024

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