NM_000081.4(LYST):c.6388G>A (p.Asp2130Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 7, 2017
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:: RCV000490083.3

Allele description [Variation Report for NM_000081.4(LYST):c.6388G>A (p.Asp2130Asn)]

NM_000081.4(LYST):c.6388G>A (p.Asp2130Asn)

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.6388G>A (p.Asp2130Asn)

HGVS:

NC_000001.11:g.235759465C>T
NG_007397.1:g.129176G>A
NM_000081.4:c.6388G>AMANE SELECT
NM_001301365.1:c.6388G>A
NP_000072.2:p.Asp2130Asn
NP_000072.2:p.Asp2130Asn
NP_001288294.1:p.Asp2130Asn
LRG_143t1:c.6388G>A
LRG_143t2:c.6388G>A
LRG_143:g.129176G>A
LRG_143p1:p.Asp2130Asn
LRG_143p2:p.Asp2130Asn
NC_000001.10:g.235922765C>T
NM_000081.2:c.6388G>A
NM_000081.3:c.6388G>A

Protein change:

D2130N

Links:

dbSNP: rs148371004

NCBI 1000 Genomes Browser:

rs148371004

Molecular consequence:

NM_000081.4:c.6388G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001301365.1:c.6388G>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
SCV000577211	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Apr 7, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000577211

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Apr 7, 2017)

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, SCV000577211.3

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

Description

The D2130N variant in the LYST gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The D2130N variant is observed in 19/66708 (0.028%) alleles from individuals of European background, in the ExAC dataset (Lek et al., 2016). The D2130N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret D2130N as a variant of uncertain significance.

#	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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