NM_000235.4(LIPA):c.6A>T (p.Lys2Asn) AND Lysosomal acid lipase deficiency

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 6, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001104686.6

Allele description [Variation Report for NM_000235.4(LIPA):c.6A>T (p.Lys2Asn)]

NM_000235.4(LIPA):c.6A>T (p.Lys2Asn)

Gene:

LIPA:lipase A, lysosomal acid type [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000235.4(LIPA):c.6A>T (p.Lys2Asn)

HGVS:

NC_000010.11:g.89247643T>A
NG_008194.1:g.9261A>T
NM_000235.4:c.6A>TMANE SELECT
NM_001127605.3:c.6A>T
NM_001288979.2:c.-120+4094A>T
NP_000226.2:p.Lys2Asn
NP_001121077.1:p.Lys2Asn
NC_000010.10:g.91007400T>A
NM_000235.2:c.6A>T

Protein change:

K2N

Links:

dbSNP: rs138408240

NCBI 1000 Genomes Browser:

rs138408240

Molecular consequence:

NM_001288979.2:c.-120+4094A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000235.4:c.6A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127605.3:c.6A>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Lysosomal acid lipase deficiency
Synonyms:: Acid cholesteryl ester hydrolase deficiency, type 2
Identifiers:: MONDO: MONDO:0800449; MedGen: C5574740; OMIM: PS278000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001261572	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV004046637	New York Genome Center	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Dec 6, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001261572

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV004046637

New York Genome Center

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Dec 6, 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	1	not provided	not provided	1	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001261572.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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
2	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From New York Genome Center, SCV004046637.1

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

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

Last Updated: Sep 29, 2024

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