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NM_000235.4(LIPA):c.891C>T (p.Ser297=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(5)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Aug 13, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000301575.6
Variation ID:
301575
Description:
single nucleotide variant
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NM_000235.4(LIPA):c.891C>T (p.Ser297=)

Allele ID
317220
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 89222514 (GRCh38) GRCh38 UCSC
10: 90982271 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.90982271G>A
NC_000010.11:g.89222514G>A
NM_000235.4:c.891C>T MANE Select NP_000226.2:p.Ser297= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:89222513:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00029
1000 Genomes Project 0.00080
Exome Aggregation Consortium (ExAC) 0.00026
The Genome Aggregation Database (gnomAD) 0.00025
Trans-Omics for Precision Medicine (TOPMed) 0.00053
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Links
ClinGen: CA5593582
dbSNP: rs145066614
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Oct 2, 2020 RCV000594326.4
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Mar 7, 2018 RCV000673075.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 26, 2020 RCV000322362.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LIPA - - GRCh38
GRCh37
315 332

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 28, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000704061.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Wolman disease
Allele origin: germline
Invitae
Accession: SCV001031295.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Oct 02, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001786514.1
Submitted: (Aug 13, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28502505)
Uncertain significance
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Wolman Disease
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000365981.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(Mar 07, 2018)
criteria provided, single submitter
Method: clinical testing
Lysosomal acid lipase deficiency
Allele origin: unknown
Counsyl
Accession: SCV000798243.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Lysosomal acid lipase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000365980.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Lysosomal acid lipase deficiency: A hidden disease among cohorts of familial hypercholesterolemia? Chora JR Journal of clinical lipidology 2017 PMID: 28502505
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=LIPA - - - -

Text-mined citations for rs145066614...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 17, 2021