chr8-18061458-C-T

Position:

• chr8-18061458-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PM5 PP3 PP5

The NM_177924.5(ASAH1):​c.704G>A​(p.Gly235Asp) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G235R) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: ASAH1 NM_177924.5 missense, splice_region
• Scores: Splicing: ADA: 0.9975
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:1
• Conservation: PhyloP100: 7.36

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM1: In a chain Acid ceramidase subunit beta (size 252) in uniprot entity ASAH1_HUMAN there are 37 pathogenic changes around while only 7 benign (84%) in NM_177924.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr8-18061686-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 545563.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 8-18061458-C-T is Pathogenic according to our data. Variant chr8-18061458-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 362375.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASAH1	NM_177924.5	c.704G>A	p.Gly235Asp	missense_variant, splice_region_variant	10/14	ENST00000637790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASAH1	ENST00000637790.2	c.704G>A	p.Gly235Asp	missense_variant, splice_region_variant	10/14	1	NM_177924.5	P2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457858 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 725582

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.02e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Apr 10, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 26, 2019	The G235D variant has been reported in an infant with contractures and joint pain that progressed to subcutaneous nodules and hoarseness of the voice who harbored another variant in the ASAH1 gene (Tocoletti et al., 2014). The G235D variant is not observed in large population cohorts (Lek et al., 2016). The G235D variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. A different missense change at this residue (G235R) has been reported as pathogenic in the published literature in association with ASAH1-related disorders (Muramatsu et al., 2002; Bashyam et al., 2014). In summary, we interpret G235D as a likely pathogenic variant. -

Farber lipogranulomatosis Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 28, 2017

The ASAH1 c.704G>A (p.Gly235Asp) variant is a missense variant that has been reported in one case study in which it is found in a compound heterozygous state with a frameshift variant in an infant who was initially diagnosed with juvenile idiopathic arthritis (Torcoletti et al. 2014). Control data are unavailable for the p.Gly235Asp variant, and it is not found in the 1000 Genomes Project, the Exome Sequencing Project or the Exome Aggregation Consortium despite being located in a region of good sequencing coverage. The variant is thus considered to be rare. Functional studies in cultured skin fibroblasts from the compound heterozygous individual demonstrated that the ceramide content was markedly elevated compared to wildtype, which is consistent with Farber disease. The evidence for this variant is limited. The p.Gly235Asp variant is therefore classified as a variant of unknown significance but suspicious for pathogenicity for Farber lipogranulomatosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.86
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.85	D;D;D;.;T;T;T;T;T;T;T;.;.;.;.;T
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.97	.;D;D;D;D;.;D;D;D;D;D;T;D;D;D;D
M_CAP	Uncertain	0.11	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.36	D
MutationAssessor	Uncertain	2.8	M;M;.;.;.;.;.;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Uncertain	0.67	T
PROVEAN	Pathogenic	-6.4	.;D;D;D;.;.;.;.;.;.;.;.;.;.;D;.
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	.;D;D;D;.;.;.;.;.;.;.;.;.;.;D;.
Sift4G	Uncertain	0.023	.;D;D;D;.;.;.;.;.;.;.;.;.;.;D;.
Polyphen		1.0	D;D;D;D;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.95, 0.95, 0.94, 0.94
MutPred		0.89		Gain of helix (P = 0.0861);Gain of helix (P = 0.0861);.;.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP		0.97
MPC		0.0097
ClinPred		1.0	D
GERP RS		5.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8
Varity_R		0.94
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.91
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs886062781; hg19: chr8-17918967;