NM_000081.4(LYST):c.10526G>A (p.Arg3509Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 17, 2020
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:: RCV001770233.2

Allele description [Variation Report for NM_000081.4(LYST):c.10526G>A (p.Arg3509Gln)]

NM_000081.4(LYST):c.10526G>A (p.Arg3509Gln)

Gene:

LYST:lysosomal trafficking regulator [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q42.3

Genomic location:

Preferred name:

NM_000081.4(LYST):c.10526G>A (p.Arg3509Gln)

HGVS:

NC_000001.11:g.235697121C>T
NG_007397.1:g.191520G>A
NM_000081.4:c.10526G>AMANE SELECT
NM_001301365.1:c.10526G>A
NP_000072.2:p.Arg3509Gln
NP_000072.2:p.Arg3509Gln
NP_001288294.1:p.Arg3509Gln
LRG_143t1:c.10526G>A
LRG_143t2:c.10526G>A
LRG_143:g.191520G>A
LRG_143p1:p.Arg3509Gln
LRG_143p2:p.Arg3509Gln
NC_000001.10:g.235860421C>T
NM_000081.2:c.10526G>A
NM_000081.3:c.10526G>A

Protein change:

R3509Q

Links:

dbSNP: rs138936105

NCBI 1000 Genomes Browser:

rs138936105

Molecular consequence:

NM_000081.4:c.10526G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001301365.1:c.10526G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002002023	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Feb 17, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002002023

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Feb 17, 2020)

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, SCV002002023.2

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Identified in the heterozygous state in a patient with acute myeloid leukemia and hemophagocytic lymphohistiocytosis in published literature, however, this patient also had a balanced translocation t(8;21;22)(q22;q22;q11.2) (Wu et al., 2018); This variant is associated with the following publications: (PMID: 30383631)

#	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: Sep 29, 2024

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