8-18059385-G-C
Variant names:
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_177924.5(ASAH1):āc.997C>Gā(p.Arg333Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,614,174 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 Likely pathogenic (ā ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 33)
Exomes š: 0.000020 ( 0 hom. )
Consequence
ASAH1
NM_177924.5 missense
NM_177924.5 missense
Scores
14
3
2
Clinical Significance
Conservation
PhyloP100: 6.01
Genes affected
ASAH1 (HGNC:735): (N-acylsphingosine amidohydrolase 1) This gene encodes a member of the acid ceramidase family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. Processing of this preproprotein generates alpha and beta subunits that heterodimerize to form the mature lysosomal enzyme, which catalyzes the degradation of ceramide into sphingosine and free fatty acid. This enzyme is overexpressed in multiple human cancers and may play a role in cancer progression. Mutations in this gene are associated with the lysosomal storage disorder, Farber lipogranulomatosis, and a neuromuscular disorder, spinal muscular atrophy with progressive myoclonic epilepsy. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PM1
In a mutagenesis_site Mildly decreased autocatalytic processing. Loss of ceramidase activity. (size 0) in uniprot entity ASAH1_HUMAN
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.958
PP5
Variant 8-18059385-G-C is Pathogenic according to our data. Variant chr8-18059385-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 585439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-18059385-G-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251460Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135898
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GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727238
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74448
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:5Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:1Uncertain:3
Uncertain significance, flagged submission | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Uncertain significance, flagged submission | clinical testing | Athena Diagnostics | Apr 12, 2018 | - - |
Uncertain significance, flagged submission | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 08, 2023 | 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. This variant disrupts the p.Arg333 amino acid residue in ASAH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27411168, 28733637). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 ASAH1 protein function. ClinVar contains an entry for this variant (Variation ID: 585439). This variant is also known as p.Arg349Gly. This missense change has been observed in individuals with Farber disease (PMID: 24355074, 28733637). This variant is present in population databases (rs543697946, gnomAD 0.04%). This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 333 of the ASAH1 protein (p.Arg333Gly). - |
Farber lipogranulomatosis Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | - | The ASAH1 c.997C>G p.Arg333Gly variant has been reported in heterozygous state in unrelated families affected with Farber lipogranulomatosis (Bashyam et. al., 2014; Yu. et al., 2018). Experimental studies have shown protein structural analysis on mutated amino acid sequence using HANSA and it is predicted that this change in sequence results in disruption in the conformation of the catalytic triad. (Bashyam et. al., 2014). This variant has been reported to the ClinVar database as Pathogenic, Likely Pathogenic and Variant of Uncertain Significance (VUS). It is reported with allele frequency of 0.006% in gnomAD database. The amino acid Arg at position 333 is changed to a Gly changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Arg333Gly in ASAH1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | literature only | Medical Affairs, Dicerna Pharmaceuticals | Jun 19, 2019 | Published data sheds additional light on variant c.997C>G suggesting the status be updated from uncertain significance to pathogenic. Four children from 3 unrelated families have been diagnosed with Farber disease associated with variant c.997C>G. Patient 1 discussed in Bashyam et al., 2014, doi: 10.1111/cge.12316, was diagnosed with Farber disease due to symptoms characteristic of Farber disease Type 1 (Gene Reviews; https://www.ncbi.nlm.nih.gov/books/NBK488189/). The child has compound heterozygous variants in the ASAH1 gene. Skin biopsy showed diffuse fibroblastic proliferation with diffuse chronic inflammatory cell infiltrates in the dermis with fat and foamy macrophages present in-between the fibroblasts which is characteristic of Farber disease. Protein structural analysis using HANSA was performed for the mutated amino acid sequence. It is predicted this change in sequence results in disruption in the conformation of the catalytic triad. Additionally, 2 siblings from a second unrelated family were were described in Bashyam et al., 2014, with Type 1 Farber disease. These sisters inherited the c.997C>G variant from their parents according to biparental segregation. Lastly, a fourth unrelated Farber disease patient was described in Cozma et al., 2017, DOI:10.1038/s41598-017-06604-2. In this patient, ceramide biomarker C26:0 was measured in samples from 10 Farber patients and 2 SMA-PME patients. It was demonstrated within this group that C26:0 Isoform 1 levels were significanly higher than the control group verifying the presence of Farber disease. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | Mar 14, 2024 | - - |
Abnormality of metabolism/homeostasis Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Kariminejad - Najmabadi Pathology & Genetics Center | Jul 10, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D;D;D;.;T;T;T;T;T;T;T;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
.;D;D;D;D;.;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;M;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Benign
T
PROVEAN
Pathogenic
.;D;D;D;.;.;.;.;.;.;.;.;.;D
REVEL
Pathogenic
Sift
Pathogenic
.;D;D;D;.;.;.;.;.;.;.;.;.;D
Sift4G
Pathogenic
.;D;D;D;.;.;.;.;.;.;.;.;.;D
Polyphen
D;D;D;D;.;.;.;.;.;.;.;.;.;.
Vest4
0.93, 0.95, 0.93
MutPred
Loss of stability (P = 0.0392);Loss of stability (P = 0.0392);.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.98
MPC
0.0061
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at