rs772684869
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_000235.4(LIPA):c.1070T>C(p.Leu357Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L357L) has been classified as Likely benign.
Frequency
Consequence
NM_000235.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPA | NM_000235.4 | c.1070T>C | p.Leu357Pro | missense_variant | 10/10 | ENST00000336233.10 | |
LIPA | NM_001127605.3 | c.1070T>C | p.Leu357Pro | missense_variant | 10/10 | ||
LIPA | NM_001288979.2 | c.722T>C | p.Leu241Pro | missense_variant | 8/8 | ||
LIPA | XM_024448023.2 | c.1070T>C | p.Leu357Pro | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPA | ENST00000336233.10 | c.1070T>C | p.Leu357Pro | missense_variant | 10/10 | 1 | NM_000235.4 | P1 | |
LIPA | ENST00000371837.5 | c.902T>C | p.Leu301Pro | missense_variant | 9/9 | 2 | |||
LIPA | ENST00000456827.5 | c.722T>C | p.Leu241Pro | missense_variant | 8/8 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251462Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135904
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727228
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
Lysosomal acid lipase deficiency Pathogenic:2Uncertain:1
Likely pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Jul 09, 2020 | - - |
Likely pathogenic, criteria provided, single submitter | research | Alexion Pharmaceuticals, Inc | Jun 01, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Jun 12, 2017 | - - |
Wolman disease Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 357 of the LIPA protein (p.Leu357Pro). This variant is present in population databases (rs772684869, gnomAD 0.008%). This missense change has been observed in individual(s) with cholesteryl ester storage disease (PMID: 7773732). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as Leu336Pro. ClinVar contains an entry for this variant (Variation ID: 552474). 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 with a positive predictive value of 80%. Experimental studies have shown that this missense change affects LIPA function (PMID: 7499245, 31131398, 31180157). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at