NM_000235.4(LIPA):c.594dup (p.Ala199fs) AND Lysosomal acid lipase deficiency

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Nov 2, 2016
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:: RCV000000100.11

Allele description [Variation Report for NM_000235.4(LIPA):c.594dup (p.Ala199fs)]

NM_000235.4(LIPA):c.594dup (p.Ala199fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000235.4(LIPA):c.594dup (p.Ala199fs)

HGVS:

NC_000010.11:g.89225178dup
NG_008194.1:g.31731dup
NM_000235.4:c.594dupMANE SELECT
NM_001127605.3:c.594dup
NM_001288979.2:c.246dup
NP_000226.2:p.Ala199fs
NP_001121077.1:p.Ala199fs
NP_001275908.1:p.Ala83fs
NC_000010.10:g.90984929_90984930insA
NC_000010.10:g.90984935dup
NM_000235.2:c.594dupT
NM_000235.3:c.594dup
NM_000235.3:c.594dupT

Note:

NCBI staff reviewed the sequence information reported in PubMed 8146180 Fig. 5 to determine the location of this allele on the current reference sequence.

Protein change:

A199fs

Links:

OMIM: 613497.0004; dbSNP: rs780495201

NCBI 1000 Genomes Browser:

rs780495201

Molecular consequence:

NM_000235.4:c.594dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127605.3:c.594dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001288979.2:c.246dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000485753	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Likely pathogenic (Nov 2, 2016)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf, Citation Link,
SCV002091388	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 22, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000485753

Counsyl

criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))

Likely pathogenic
(Nov 2, 2016)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV002091388

Natera, Inc.

no assertion criteria provided

Pathogenic
(Sep 22, 2020)

germline

clinical testing

Help

Summary from all submissions

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

Citations

PubMed

Mutations at the lysosomal acid cholesteryl ester hydrolase gene locus in Wolman disease.

Anderson RA, Byrum RS, Coates PM, Sando GN.

Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2718-22.

PubMed [citation]

PMID:: 8146180
PMCID:: PMC43441

Details of each submission

From Counsyl, SCV000485753.2

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

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

From Natera, Inc., SCV002091388.1

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

Last Updated: Oct 13, 2024

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