U.S. flag

An official website of the United States government

NM_000235.4(LIPA):c.599T>C (p.Leu200Pro) AND Wolman disease

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jul 3, 2023
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:
RCV000000095.11

Allele description [Variation Report for NM_000235.4(LIPA):c.599T>C (p.Leu200Pro)]

NM_000235.4(LIPA):c.599T>C (p.Leu200Pro)

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.599T>C (p.Leu200Pro)
Other names:
L179P
HGVS:
  • NC_000010.11:g.89225168A>G
  • NG_008194.1:g.31736T>C
  • NM_000235.4:c.599T>CMANE SELECT
  • NM_001127605.3:c.599T>C
  • NM_001288979.2:c.251T>C
  • NP_000226.2:p.Leu200Pro
  • NP_001121077.1:p.Leu200Pro
  • NP_001275908.1:p.Leu84Pro
  • NC_000010.10:g.90984925A>G
  • NM_000235.2:c.599T>C
  • NM_000235.3:c.599T>C
  • P38571:p.Leu200Pro
Protein change:
L200P; LEU179PRO
Links:
UniProtKB: P38571#VAR_004250; OMIM: 613497.0001; dbSNP: rs121965086
NCBI 1000 Genomes Browser:
rs121965086
Molecular consequence:
  • NM_000235.4:c.599T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127605.3:c.599T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001288979.2:c.251T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Wolman disease (WOLD)
Synonyms:
Acid cholesteryl ester hydrolase deficiency, Wolman type; Acid lipase disease; Wolman disease, CESD; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0019148; MedGen: C0043208; OMIM: 620151

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020238OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 1995)
germlineliterature only

PubMed (2)
[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.,

SCV000931711Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jul 3, 2023)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV003844837Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Feb 16, 2023)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

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

Characterization of lysosomal acid lipase by site-directed mutagenesis and heterologous expression.

Sheriff S, Du H, Grabowski GA.

J Biol Chem. 1995 Nov 17;270(46):27766-72.

PubMed [citation]
PMID:
7499245
See all PubMed Citations (9)

Details of each submission

From OMIM, SCV000020238.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Wolman Disease

In a proband with Wolman disease (WOLD; 620151) from a nonconsanguineous family, Anderson et al. (1994) detected a T-to-C transition at nucleotide 639 of the LIPA gene that resulted in a nonconservative missense mutation, leu179 to pro (L179P). This mutation was found in compound heterozygosity with a single-base insertion resulting in a null allele (613497.0004). The proband had had 2 older sibs with Wolman disease. Anderson et al. (1994) noted that the L179P mutation is located 26 amino acids from the predicted active site of lysosomal acid lipase and was expected to disrupt the alpha-helical structure in a highly conserved region of the protein.

Cholesteryl Ester Storage Disease

Maslen and Illingworth (1993) and Maslen et al. (1995) found the L179P mutation in 2 sibs with cholesteryl ester storage disease (CESD; 278000). In these sibs the L179P mutation, inherited from the mother, was found in compound heterozygosity with a splice site mutation that resulted in skipping of exon 8 of lysosomal acid lipase (613497.0002). Maslen et al. (1995) compared the phenotypes of other patients carrying the L179P or the splice site mutation described by them and concluded that the L179P mutant allele apparently does not make a substantial contribution to cholesteryl ester hydrolase activity.

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

From Invitae, SCV000931711.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LIPA protein function. This missense change has been observed in individual(s) with cholesterol ester storage disease (CESD) or Wolman disease (PMID: 8146180, 8598644, 8617513, 23430518). It has also been observed to segregate with disease in related individuals. This variant is also known as L179P. ClinVar contains an entry for this variant (Variation ID: 77). Experimental studies have shown that this missense change affects LIPA function (PMID: 7499245, 10562460). For these reasons, this variant has been classified as Pathogenic. This variant is present in population databases (rs121965086, gnomAD 0.003%). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 200 of the LIPA protein (p.Leu200Pro).

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003844837.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Variant summary: LIPA c.599T>C (p.Leu200Pro) results in a non-conservative amino acid change located in the Alpha/beta hydrolase fold-1 domain (IPR000073) of the encoded protein sequence. This variant is also known as L179P. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251462 control chromosomes (gnomAD). c.599T>C has been reported in the literature in individuals affected with Lysosomal Acid Lipase Deficiency (examples: Pullinger_2015, Ambler_2012, Anderson_1994, Maslen_1995). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (example: Vinje_2019) . Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Jun 23, 2024