NM_022166.4(XYLT1):c.1730_1733dup (p.Asp578delinsGluTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 21, 2024
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:: RCV000489929.2

Allele description [Variation Report for NM_022166.4(XYLT1):c.1730_1733dup (p.Asp578delinsGluTer)]

NM_022166.4(XYLT1):c.1730_1733dup (p.Asp578delinsGluTer)

Genes:

LOC102723692:uncharacterized LOC102723692 [Gene]
XYLT1:xylosyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p12.3

Genomic location:

Preferred name:

NM_022166.4(XYLT1):c.1730_1733dup (p.Asp578delinsGluTer)

HGVS:

NC_000016.10:g.17138387_17138390dup
NG_015843.2:g.337493_337496dup
NM_022166.4:c.1730_1733dupMANE SELECT
NP_071449.1:p.Asp578delinsGluTer
NC_000016.9:g.17232244_17232247dup
NG_015843.1:g.337493_337496dup
NM_022166.3:c.1730_1733dup
NM_022166.3:c.1730_1733dupATGA
NR_135179.1:n.292_295dup

Links:

OMIM: 608124.0012; dbSNP: rs1085307563

NCBI 1000 Genomes Browser:

rs1085307563

Molecular consequence:

NR_135179.1:n.292_295dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_022166.4:c.1730_1733dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000576728	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 21, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000576728

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 21, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000576728.5

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30554721)

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

Last Updated: Oct 8, 2024

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