chr17-3481609-AAT-A
Position:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000049.4(ASPA):c.244_245del(p.Met82ValfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
ASPA
NM_000049.4 frameshift
NM_000049.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.669
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-3481609-AAT-A is Pathogenic according to our data. Variant chr17-3481609-AAT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 189005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASPA | NM_000049.4 | c.244_245del | p.Met82ValfsTer7 | frameshift_variant | 2/6 | ENST00000263080.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASPA | ENST00000263080.3 | c.244_245del | p.Met82ValfsTer7 | frameshift_variant | 2/6 | 1 | NM_000049.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spongy degeneration of central nervous system Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | This sequence change creates a premature translational stop signal (p.Met82Valfs*7) in the ASPA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ASPA are known to be pathogenic (PMID: 12638939). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Canavan disease (PMID: 16854607). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 189005). - |
Likely pathogenic, criteria provided, single submitter | literature only | Counsyl | Oct 10, 2014 | - - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2021 | The c.244_245delAT (p.M82Vfs*7) alteration, located in exon 2 (coding exon 2) of the ASPA gene, consists of a deletion of 2 nucleotides from position 244 to 245, causing a translational frameshift with a predicted alternate stop codon after 7 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from the Genome Aggregation Database (gnomAD), the ASPA c.244_245delAT alteration was not observed, with coverage at this position. This mutation has been reported in the homozygous state in a patient with Canavan disease (Zeng, 2006). Based on the available evidence, this alteration is classified as pathogenic. - |
Computational scores
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Splicing
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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