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NM_000235.4(LIPA):c.894G>A (p.Gln298=) AND Cholesteryl ester storage disease

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Sep 25, 2024
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:
RCV001823874.8

Allele description [Variation Report for NM_000235.4(LIPA):c.894G>A (p.Gln298=)]

NM_000235.4(LIPA):c.894G>A (p.Gln298=)

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.894G>A (p.Gln298=)
Other names:
934G>A; E8SJ; p.Gln298=
HGVS:
  • NC_000010.11:g.89222511C>T
  • NG_008194.1:g.34393G>A
  • NM_000235.4:c.894G>AMANE SELECT
  • NM_001127605.3:c.894G>A
  • NM_001288979.2:c.546G>A
  • NP_000226.2:p.Gln298=
  • NP_001121077.1:p.Gln298=
  • NP_001275908.1:p.Gln182=
  • NC_000010.10:g.90982268C>T
  • NM_000235.2:c.894G>A
  • NM_000235.3:c.894G>A
  • NM_001127605.1:c.894G>A
  • NP_001121077.1:p.=
Nucleotide change:
934G-A
Links:
OMIM: 613497.0002; dbSNP: rs116928232
NCBI 1000 Genomes Browser:
rs116928232
Molecular consequence:
  • NM_000235.4:c.894G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127605.3:c.894G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001288979.2:c.546G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Functional consequence:
exon loss [PubMedVariation Ontology: 0381]
Observations:
1

Condition(s)

Name:
Cholesteryl ester storage disease (CESD)
Identifiers:
MONDO: MONDO:0019149; MedGen: C0008384; Orphanet: 75234; OMIM: 278000

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020241OMIM
no assertion criteria provided
Pathogenic
(Apr 1, 1996)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

Maslen, C. L., Illingworth, D. R. Molecular genetics of cholesterol ester hydrolase deficiency. (Abstract) Am. J. Hum. Genet. 53 (suppl.): A926, 1993.,

SCV004698093Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 5, 2024)
unknownclinical testing

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

SCV005042764Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

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

SCV005051850Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 1, 2024)
germlinecuration

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

SCV005373793KardioGenetik, Herz- und Diabeteszentrum NRW
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 25, 2024)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedcuration
not providedunknownyes1not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic and biochemical evidence that CESD and Wolman disease are distinguished by residual lysosomal acid lipase activity.

Aslanidis C, Ries S, Fehringer P, Büchler C, Klima H, Schmitz G.

Genomics. 1996 Apr 1;33(1):85-93.

PubMed [citation]
PMID:
8617513

Occurrence of a mutation associated with Wolman disease in a family with cholesteryl ester storage disease.

Maslen CL, Babcock D, Illingworth DR.

J Inherit Metab Dis. 1995;18(5):620-3.

PubMed [citation]
PMID:
8598644
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000020241.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a 12-year-old patient with cholesteryl ester storage disease (CESD; 278000) from a nonconsanguineous Polish-German family, Klima et al. (1993) detected a 72-bp in-frame deletion resulting in the loss of amino acid codons 254 through 277. Analysis of genomic DNA revealed that the 72 bp represented an exon, indicating that the deletion in the mRNA was caused by defective splicing. Sequence analysis of the patient's genomic DNA revealed a G-to-A substitution in the last nucleotide of the 72-bp exon on 1 allele. No normal-sized mRNA was detectable in the propositus even though he was not homozygous for the splice site mutation. Klima et al. (1993) concluded that the patient was compound heterozygous for the splice site mutation and a null allele. The patient showed LIPA activity in cultured skin fibroblasts approximately 9% of normal. Hepatosplenomegaly had been present since age 5 years.

Aslanidis et al. (1996) restudied the patient of Klima et al. (1993) and defined the splice site mutation as a G-to-A mutation at position -1 of the splice donor site following exon 8, resulting in incorrect splicing and the removal of the 72-bp exon 8 of the LIPA gene. They determined that the other allele of the patient carried a premature termination mutation (613497.0003) as well as the L179P mutation (613497.0001); the LIPA mRNA was rendered unstable by the premature stop codon. Aslanidis et al. (1996) demonstrated that the splice site mutation allowed the production of approximately 3 to 4% of correctly spliced mRNA relative to wildtype. Aslanidis et al. (1996) also identified a mutation at the same splice donor site, and also resulting in deletion of exon 8, in 2 sibs with Wolman disease; that mutation, at the +1 position, allowed no correct splicing, and patient fibroblasts were devoid of enzymatic activity. See 613497.0005.

In 2 sibs with CESD, Maslen and Illingworth (1993) and Maslen et al. (1995) identified compound heterozygosity for this splice site mutation in the LIPA gene, inherited from their father, and the L179P mutation (613497.0001). The affected children were a sister and brother who presented with idiopathic hepatomegaly at ages 6 and 8 years, respectively. Subsequent analyses indicated that they also had hypercholesterolemia and a severe reduction in cholesteryl ester hydrolase activity in cultured fibroblasts.

Muntoni et al. (1995) observed homozygosity for the splice site mutation (Klima et al., 1993) in a Spanish kindred with cholesterol ester storage disease. Exon 8 of the LIPA gene was deleted.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV004698093.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria applied: PM3_VSTR,PS3,PP4

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV005042764.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The splice region and synonymous c.894G>Ap.Gln298 variant in LIPA gene has been reported previously in homozygous state in individuals affected with cholesteryl ester storage disease and is estimated to be carried by 40-60% of affected individuals Bernstein et al., 2013. Experimental studies have shown that this variant affects LIPA function Pagani et al., 1998. This variant is reported with the allele frequency of 0.09% in the gnomAD Exomes and novel in 1000 Genomes. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic multiple submitters. This variant creates a cryptic splice donor site within exon 8 and causes abnormal gene splicing. The spliceAI tool predicts that this splice site variant is damaging. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV005051850.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From KardioGenetik, Herz- und Diabeteszentrum NRW, SCV005373793.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 26, 2024