NM_000081.4(LYST):c.6388G>A (p.Asp2130Asn) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 11, 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:: RCV002526027.2

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)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003710626	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003710626

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 11, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003710626.2

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

Description

The c.6388G>A (p.D2130N) alteration is located in exon 23 (coding exon 21) of the LYST gene. This alteration results from a G to A substitution at nucleotide position 6388, causing the aspartic acid (D) at amino acid position 2130 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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 8, 2024

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