rs28940279

Positions:

• chr17-3499000-A-C

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 13P and 1B. PM1 PM2 PP3 PP5_Very_Strong BP4

The NM_000049.4(ASPA):​c.854A>C​(p.Glu285Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000221 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00022 (0 hom.)
• Consequence: ASPA NM_000049.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:17 O:2
• Conservation: PhyloP100: 8.94

Genes affected

ASPA (HGNC:756): (aspartoacylase) This gene encodes an enzyme that catalyzes the conversion of N-acetyl_L-aspartic acid (NAA) to aspartate and acetate. NAA is abundant in the brain where hydrolysis by aspartoacylase is thought to help maintain white matter. This protein is an NAA scavenger in other tissues. Mutations in this gene cause Canavan disease. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

SPATA22 (HGNC:30705): (spermatogenesis associated 22) Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 3 uncertain in NM_000049.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: Multiple lines of computational evidence support a deleterious effect 9: AlphaMissense, BayesDel_addAF, BayesDel_noAF, Eigen, M_CAP, MutationAssessor, phyloP100way_vertebrate, PROVEAN, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• PP5: Variant 17-3499000-A-C is Pathogenic according to our data. Variant chr17-3499000-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 2605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-3499000-A-C is described in Lovd as [Pathogenic]. Variant chr17-3499000-A-C is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.1546188). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASPA	NM_000049.4	c.854A>C	p.Glu285Ala	missense_variant	6/6	ENST00000263080.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASPA	ENST00000263080.3	c.854A>C	p.Glu285Ala	missense_variant	6/6	1	NM_000049.4	P1
ASPA	ENST00000456349.6	c.854A>C	p.Glu285Ala	missense_variant	7/7	1		P1
SPATA22	ENST00000541913.5	c.-74+14412T>G		intron_variant		2
SPATA22	ENST00000570318.1	c.-74+14611T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.000263 AC: 40 AN: 152218 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000430 AC: 108 AN: 251434 Hom.: 0 AF XY: 0.000493 AC XY: 67 AN XY: 135892

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00923

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000528

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.000216 AC: 316 AN: 1461882 Hom.: 0 Cov.: 31 AF XY: 0.000238 AC XY: 173 AN XY: 727240

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00926

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000315

Gnomad4 OTH exome AF: 0.000646

GnomAD4 genome AF: 0.000263 AC: 40 AN: 152218 Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18 AN XY: 74360

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00923

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000541 Hom.: 0

Bravo AF: 0.000257

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.000354 AC: 43

EpiCase AF: 0.000218

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Spongy degeneration of central nervous system Pathogenic:12 Other:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 01, 1994	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 07, 2021	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpreted as Pathogenic and reported on 02-10-2017 by Lab or GTR ID 1006. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Likely pathogenic, no assertion criteria provided	curation	Reproductive Health Research and Development, BGI Genomics	Jan 06, 2020	NM_000049.2:c.854A>C in the ASPA gene has an allele frequency of 0.009 in Ashkenazi Jewish subpopulation in the gnomAD database. Functional studies demonstrate that c.854A>C has disturbed the active site architecture, leading to altered substrate binding and lower catalytic activity (PMID: 25003821). Elpeleg et al reported that 18 patients with canavan disease, who are homozygous for this variant (PMID: 8037206). Pathogenic computational verdict because pathogenic predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, PrimateAI, REVEL and SIFT. Taken together, we interprete this variant as a Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PS3; PM3; PP3; PP4. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 12, 2019	NM_000049.2(ASPA):c.854A>C(E285A) is classified as pathogenic in the context of Canavan disease. Sources cited for classification include the following: PMID 8252036, 8037206 and 22850825. Classification of NM_000049.2(ASPA):c.854A>C(E285A) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 30, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jun 24, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Canavan disease (MIM#271900). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to alanine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (113 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and very highly conserved with a major amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This is a common mutation reported in Askenazi Jewish population and it has been reported multiple times as pathogenic (ClinVar, PMID: 34011350). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 02, 2014	The p.Glu285Ala variant in ASPA is one of the most frequent pathogenic variants implicated in Canavan disease and has been reported in at least 19 Ashkenazi Jew ish individuals with the disease. Most of these individuals were homozygous (Kau l 1993). This variant has also been identified 0.04% (43/120,682) of chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSN P rs28940279). In vitro functional studies also provide evidence that the p.Glu 285Ala variant may impact protein function, leading to <1% of wild type enzymati c activity (Zano 2013). In summary, this variant meets our criteria to be classi fied as pathogenic for Canavan disease in an autosomal recessive manner based up on its biallelic occurrence in affected individuals and functional impact. -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 285 of the ASPA protein (p.Glu285Ala). This variant is present in population databases (rs28940279, gnomAD 0.9%). This missense change has been observed in individual(s) with Canavan disease (PMID: 8037206, 8252036). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2605). 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 ASPA protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ASPA function (PMID: 25003821). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 24, 2018	The ASPA c.854A>C (p.Glu285Ala) missense variant has been reported in two studies in which it was found in a total of 19 individuals with Canavan disease. The p.Glu285Ala variant was identified in a homozygous state in 12 individuals, in a compound heterozygous state in two individuals and in a heterozygous state in five individuals in whom the second variant was not identified (Kaul et al. 1993; Zano et al. 2013). The p.Glu285Ala variant along with a second missense variant (p.Tyr231Ter), accounts for 98% of disease-causing alleles in the Ashkenazi Jewish population and 3% of alleles in non-Ashkenazi Jewish populations (Matalon and Michals-Matalon, 1999). The p.Glu285Ala variant was absent from 84 controls and is reported at a frequency of 0.009257 in the Ashkenazi Jewish population of the Genome Aggregation Database. Functional studies in vitro have shown the enzyme activity to be 0.02% of the wild type (Zano et al. 2013). Based on the collective evidence, the p.Glu285Ala variant is classified as pathogenic for Canavan disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 17, 2021	- -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 02, 2022	Expression studies found that E285A is associated with 0.3% of wild-type aspartoacylase enzyme activity as well as reduced thermal and conformational stability (Zano et al., 2013); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23233226, 25003821, 22850825, 25333069, 21228398, 30609409, 20301412, 8037206, 31589614, 33304759, 8252036) -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 15, 2016	- -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The ASPA p.Glu285Ala variant is a well-known causal variant for autosomal recessive Canavan disease (CD), and is known to be associated with 84% of CD alleles in the Ashkenazi Jewish population (Matalon_1997_PMID: 10464621). This variant was identified in dbSNP (ID: rs28940279), Clinvitae, MutDB, LOVD 3.0 and ClinVar (reported as pathogenic for CD by Invitae, Emory, Partners Laboratory for Molecular Medicine, GeneDx, Counsyl and Integrated Genetics). The variant was identified in control databases in 113 of 282830 chromosomes at a frequency of 0.0004 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 96 of 10370 chromosomes (freq: 0.009257), Other in 7 of 7228 chromosomes (freq: 0.000969), African in 2 of 24964 chromosomes (freq: 0.00008) and European (non-Finnish) in 8 of 129156 chromosomes (freq: 0.000062); it was not observed in the Latino, East Asian, European (Finnish), and South Asian populations. Multiple functional studies have shown the p.Glu285Ala mutation to cause loss of ASPA enzymatic activity (Hershfield_2007_PMID: 17391648; Mendes_2017_PMID: 28101991). The p.Glu285 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, and MutationTaster) suggest that the variant impacts the protein. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 06, 2017

The p.E285A pathogenic mutation (also known as c.854A>C), located in coding exon 6 of the ASPA gene, results from an A to C substitution at nucleotide position 854. The glutamic acid at codon 285 is replaced by alanine, an amino acid with dissimilar properties. This is the most common ASPA mutation in the Ashkenazi Jewish population. In one study of 17 Ashkenazi Jewish individuals with Canavan disease, 12 probands were homozygous for this mutation (parental carrier status confirmed in 3 cases) and 5 probands were heterozygous for this mutation (Kaul R et al. Nat. Genet., 1993 Oct;5:118-23). A study of the crystal structure of p.E285A mutant protein showed that loss of hydrogen bonding disturbs the active site architecture, leading to altered substrate binding and lower catalytic activity (Wijayasinghe YS et al. Biochemistry, 2014 Aug;53:4970-8). Based on the supporting evidence, p.E285A is interpreted as a disease-causing mutation. -

Canavan Disease, Familial Form Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jun 25, 2016

Variant summary: The ASPA c.854A>C (p.Glu285Ala) variant involves the alteration of a conserved nucleotide. Glu285 is predicted to be part of the catalytic domain of aspartoacylase with the catalytic center of aspartoacylase involves a triad of Ser, His and Glu residues. 4/4 in silico tools predict a damaging outcome for this variant . Functional studies show that patients with this variant have very low enzyme activity. This variant was found in 43/120850 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.000633 (42/66354). These frequencies are lower than the estimated maximal expected allele frequency of a pathogenic ASPA variant (0.0079057). Furthermore, this variant is a commonly known AJ founder mutation in the literature. The variant has been identified in many compound heterozygous and homozygous patients in the literature. In addition, multiple clinical diagnostic laboratories classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.58
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.92	D;D
Eigen	Pathogenic	0.70
Eigen_PC	Uncertain	0.58
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Pathogenic	0.38	D
MetaRNN	Benign	0.15	T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.4	M;M
MutationTaster	Benign	1.0	A;A;A
PrimateAI	Uncertain	0.63	T
PROVEAN	Pathogenic	-5.6	D;D
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.82
MVP		0.99
MPC		0.42
ClinPred		0.27	T
GERP RS		4.7
Varity_R		0.90
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs28940279; hg19: chr17-3402294; COSMIC: COSV99036550;