8-18059385-G-C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong

The NM_177924.5(ASAH1):ā€‹c.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

Scores

14
3
2

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5U:3

Conservation

PhyloP100: 6.01
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ASAH1NM_177924.5 linkc.997C>G p.Arg333Gly missense_variant Exon 12 of 14 ENST00000637790.2 NP_808592.2 Q13510-1Q53H01A8K0B6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ASAH1ENST00000637790.2 linkc.997C>G p.Arg333Gly missense_variant Exon 12 of 14 1 NM_177924.5 ENSP00000490272.1 Q13510-1

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152176
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000827
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000557
AC:
14
AN:
251460
Hom.:
0
AF XY:
0.0000736
AC XY:
10
AN XY:
135898
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000392
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.0000198
AC:
29
AN:
1461880
Hom.:
0
Cov.:
32
AF XY:
0.0000289
AC XY:
21
AN XY:
727238
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000313
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152294
Hom.:
0
Cov.:
33
AF XY:
0.0000269
AC XY:
2
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000827
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000959
Hom.:
0
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ExAC
AF:
0.0000576
AC:
7

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 submissionclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Uncertain significance, flagged submissionclinical testingAthena DiagnosticsApr 12, 2018- -
Uncertain significance, flagged submissionclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Likely pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpSep 08, 2023In 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 submitterclinical testingNeuberg 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 submitterliterature onlyMedical Affairs, Dicerna PharmaceuticalsJun 19, 2019Published 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 submitterclinical testingGenomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research CentreMar 14, 2024- -
Abnormality of metabolism/homeostasis Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingKariminejad - Najmabadi Pathology & Genetics CenterJul 10, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Pathogenic
0.38
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.95
D;D;D;.;T;T;T;T;T;T;T;.;.;.
Eigen
Pathogenic
0.93
Eigen_PC
Pathogenic
0.84
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
0.97
.;D;D;D;D;.;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.39
D
MetaRNN
Pathogenic
0.96
D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
0.70
D
MutationAssessor
Pathogenic
3.4
M;M;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Benign
0.45
T
PROVEAN
Pathogenic
-6.2
.;D;D;D;.;.;.;.;.;.;.;.;.;D
REVEL
Pathogenic
0.95
Sift
Pathogenic
0.0
.;D;D;D;.;.;.;.;.;.;.;.;.;D
Sift4G
Pathogenic
0.0
.;D;D;D;.;.;.;.;.;.;.;.;.;D
Polyphen
1.0
D;D;D;D;.;.;.;.;.;.;.;.;.;.
Vest4
0.93, 0.95, 0.93
MutPred
0.89
Loss of stability (P = 0.0392);Loss of stability (P = 0.0392);.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.98
MPC
0.0061
ClinPred
0.95
D
GERP RS
5.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.97
gMVP
0.98

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs543697946; hg19: chr8-17916894; API