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NM_000235.4(LIPA):c.309C>A (p.Ser103Arg) AND Lysosomal acid lipase deficiency

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jun 1, 2019
Review status:
criteria provided, conflicting classifications
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:
RCV000670582.6

Allele description [Variation Report for NM_000235.4(LIPA):c.309C>A (p.Ser103Arg)]

NM_000235.4(LIPA):c.309C>A (p.Ser103Arg)

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.309C>A (p.Ser103Arg)
HGVS:
  • NC_000010.11:g.89228319G>T
  • NG_008194.1:g.28585C>A
  • NM_000235.4:c.309C>AMANE SELECT
  • NM_001127605.3:c.309C>A
  • NM_001288979.2:c.-40C>A
  • NP_000226.2:p.Ser103Arg
  • NP_001121077.1:p.Ser103Arg
  • NC_000010.10:g.90988076G>T
  • NC_000010.10:g.90988076G>T
  • NM_000235.2:c.309C>A
Protein change:
S103R
Links:
dbSNP: rs766364179
NCBI 1000 Genomes Browser:
rs766364179
Molecular consequence:
  • NM_001288979.2:c.-40C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000235.4:c.309C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127605.3:c.309C>A - missense variant - [Sequence Ontology: SO:0001583]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000795451Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Uncertain significance
(Nov 8, 2017)
unknownclinical testing

Citation Link,

SCV000999865Alexion Pharmaceuticals, Inc
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jun 1, 2019)
germlineresearch

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedresearch

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

Large-scale functional LIPA variant characterization to improve birth prevalence estimates of lysosomal acid lipase deficiency.

Del Angel G, Hutchinson AT, Jain NK, Forbes CD, Reynders J.

Hum Mutat. 2019 Nov;40(11):2007-2020. doi: 10.1002/humu.23837. Epub 2019 Jul 12.

PubMed [citation]
PMID:
31180157
PMCID:
PMC6852163

Details of each submission

From Counsyl, SCV000795451.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Alexion Pharmaceuticals, Inc, SCV000999865.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024