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NM_000235.4(LIPA):c.111+1G>A AND Lysosomal acid lipase deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 23, 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:
RCV003225126.8

Allele description [Variation Report for NM_000235.4(LIPA):c.111+1G>A]

NM_000235.4(LIPA):c.111+1G>A

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.111+1G>A
HGVS:
  • NC_000010.11:g.89247537C>T
  • NG_008194.1:g.9367G>A
  • NM_000235.4:c.111+1G>AMANE SELECT
  • NM_001127605.3:c.111+1G>A
  • NM_001288979.2:c.-120+4200G>A
  • NC_000010.10:g.91007294C>T
  • NM_000235.3:c.111+1G>A
Links:
dbSNP: rs762960877
NCBI 1000 Genomes Browser:
rs762960877
Molecular consequence:
  • NM_001288979.2:c.-120+4200G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000235.4:c.111+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001127605.3:c.111+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003921865Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Feb 23, 2022) 		maternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV003921865.1

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

Description

0102 - Loss of function is a known mechanism of disease in this gene and is associated with cholesteryl ester storage disease (CEST) and Wolman disease (MIM#278000). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (2 heterozygotes, 0 homozygotes). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0704 - Another canonical splice site variant comparable to the one identified in this case has limited previous evidence for pathogenicity. A different variant in the same canonical splice site, c.111+2T>G, has been reported as likely pathogenic in ClinVar. (SP) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individual. This variant has been submitted once as likely pathogenic to ClinVar. (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Sep 29, 2024