NM_000235.4(LIPA):c.894G>A (p.Gln298=) AND not provided

Germline classification:: Pathogenic (8 submissions)
Last evaluated:: Mar 1, 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:: RCV000478829.32

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:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000342914	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Aug 22, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10562460, 22227072, 7751811, 8254026 Citation Link,
SCV000568149	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 12, 2020)	germline	clinical testing	Citation Link,
SCV001807452	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001917978	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001975876	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely pathogenic	germline	clinical testing
SCV002017148	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 29, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002525801	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003916623	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Mar 1, 2023)	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	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	16	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Lysosomal acid lipase mutations that determine phenotype in Wolman and cholesterol ester storage disease.

Anderson RA, Bryson GM, Parks JS.

Mol Genet Metab. 1999 Nov;68(3):333-45.

PubMed [citation]

PMID:: 10562460

Lysosomal lipase deficiency: molecular characterization of eleven patients with Wolman or cholesteryl ester storage disease.

Fasano T, Pisciotta L, Bocchi L, Guardamagna O, Assandro P, Rabacchi C, Zanoni P, Filocamo M, Bertolini S, Calandra S.

Mol Genet Metab. 2012 Mar;105(3):450-6. doi: 10.1016/j.ymgme.2011.12.008. Epub 2011 Dec 17.

PubMed [citation]

PMID:: 22227072

See all PubMed Citations (5)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000342914.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	11	not provided	not provided	clinical testing	PubMed (4)

#	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		11	not provided	not provided	not provided

From GeneDx, SCV000568149.6

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

Description

Published functional studies demonstrate abnormal splicing resulting in an in-frame skipping of exon 8, with 3-5% of mRNA being spliced correctly (Fasano et al., 2012); This variant is associated with the following publications: (PMID: 8254026, 10562460, 7751811, 21757691, 26350820, 27423329, 28502505, 30249571, 32093730, 22227072, 19307143, 23424026, 25722898, 22795295, 24072694, 16255772, 29884776, 25852113, 30548430, 30684275, 28502515, 29982809, 30056760, 29958253, 32382506, 31980526, 34426522, 33857477, 31589614, 33108087, 33269076, 7759067, 32432142, 32531373)

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001807452.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001917978.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001975876.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002017148.3

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV002525801.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	PubMed (1)

Description

PS3, PS4_moderate, PM2, PP3, PP4

#	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		5	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV003916623.13

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

Description

LIPA: PP1:Strong, PS3, PP3, PP4

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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