The ASPA NM_000049.4:c.854A>C (NP_000040.1:p.(Glu285Ala)) missense variant has previously been reported in somatic cancers (COSMIC; COSV99036550, n = 1 time). Experimental evidence: Purified E285A showed 0.02 U/mg activity, only 0.3% of native ASPA activity in a variant-specific assay. Based on available guidelines, this variant is considered to be Likely Pathogenic.
Five-step scale from benign to pathogenic. This variant is likely pathogenic. Select a step to read what it means.
Likely pathogenic.A likely pathogenic classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.ASPA encodes aspartoacylase, an enzyme that breaks down N-acetylaspartic acid into aspartate and acetate, helping maintain brain white matter. Changes in ASPA cause Canavan disease, a neurological disorder. No established role in cancer is known.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, moderate: purified E285A showed 0.02 U/mg activity, only 0.3% of native ASPA activity in a variant-specific assay.
Met: 18/18 affected patients versus 15/879 controls; continuity-corrected OR 2063.65 (95% CI 118.94-35805.20), exceeding the OR > 5 threshold with CI excluding 1.
Met at supporting strength: an affected Canavan disease patient carried c.854A>C compound heterozygously with IVS4+1G>T, documenting an in-trans pathogenic partner.
Met strong: missense REVEL score 0.946 meets the PP3 strong threshold of >=0.932.
No benign criterion marked as applied in the recorded assessment.
Likely Pathogenic: PS4 strong plus PS3 moderate satisfy the generic ACMG/AMP rule, with additional PM3 supporting and PP3 strong evidence.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 356 / 1,614,100 alleles. Recorded AF 0.000220556. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 0.000399533; MAF= 0.03995%, 113/282830 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00925747; MAF= 0.92575%, 96/10370 alleles, homozygotes = 0); grpmax FAF= 2.293e-05.
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.946. Refer to the recorded PP3/BP4 rationale for interpretation.
19 Pathogenic · 1 Likely pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has previously been reported in somatic cancers (COSMIC; COSV99036550, n = 1 times).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 10 not met · 10 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The exact E285A variant has strong directionally consistent biochemical evidence of impaired ASPA function, but the available single study does not support escalation beyond moderate PS3 under a validated clinical-laboratory reproducibility standard.
No evidence supports BS3.
PS4 is met at strong strength from an exact-variant case-control comparison in PMID 8037206; PP4 and BP5 remain not assessed because required patient-level phenotype or alternate-molecular-basis evidence is absent; PP5 and BP6 are not met because no exact-variant ClinVar expert-panel classification exists.
Only PP3 and BP4 were adjudicated. The variant is missense, so REVEL was the sole applicable computational path; SpliceAI was not used for either criterion, and BayesDel was unavailable under the generic calibration rule.
No criteria match.
PS3 is met at moderate strength. The exact variant, NM_000049.4:c.854A>C (p.Glu285Ala/E285A), was tested as a purified human ASPA clinical mutant expressed in Pichia pastoris. In a coupled enzyme assay, E285A had specific activity of 0.02 U/mg, corresponding to 0.3% of native aspartoacylase activity. The study also compared thermal stability (48.5°C versus 59.9°C for native enzyme) and conformational stability (125 mM versus 1,150 mM urea), providing orthogonal biochemical evidence of impaired protein function. This is a biologically relevant, variant-specific in-vitro assay with a native-protein comparator, but the available record does not establish reproducibility and robustness in a clinical diagnostic laboratory setting or provide multiple independent validated assay systems; therefore PS3 is not escalated to strong.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PS4 is met. The PS4-indexed paper PMID 8037206 reports an exact-variant case-control comparison: all 18 affected Ashkenazi Jewish patients were homozygotes for the C854 mutation, while 15 of 879 healthy Ashkenazi Jewish controls were heterozygotes. Because the case table has zero non-carriers, I applied a Haldane-Anscombe 0.5 continuity correction to the 2x2 carriage table (18.5, 0.5; 15.5, 864.5), giving OR = 2063.65 and an approximate 95% CI of 118.94-35805.20. Thus OR > 5.0 and the confidence interval excludes 1.0. PMID 25668701 was also checked as the other PS4-indexed paper; its abstract is a review of Canavan disease across Arab populations and does not report exact c.854A>C case-control counts. The two PS4-indexed PMID keys are absent from source_registry.json, so the paper citation requires human registry repair before automated audit acceptance.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
PM3 is met at supporting strength. Canavan disease is an autosomal recessive disorder. PMID:16854607 reports the exact ASPA E285A variant, corresponding to NM_000049.4:c.854A>C (p.Glu285Ala), in an affected patient with a compound-heterozygous genotype consisting of E285A and IVS4+1G>T. This documents the queried variant in trans with a second disease-associated ASPA variant in an affected individual; the same paper also reports E285A homozygosity in another affected patient, which is not the basis for PM3.
For recessive disorders, detected in trans with a pathogenic variant
NM_000049.4:c.854A>C is a missense variant, p.(Glu285Ala), so the governing generic rule selects the missense REVEL path only. The REVEL score is 0.946, which meets the supplied PP3 strong threshold of >= 0.932 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997). The SpliceAI max delta of 0.054 is not used for PP3 because splice prediction is not the applicable path for a missense variant, and the BayesDel score is not usable because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (strong): >= 0.932 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
PM2 is not met under the supplied generic supporting threshold. The variant is present in both default all-comers gnomAD datasets: gnomAD v4.1 total AF is 0.000220556 (356/1,614,100 alleles), and gnomAD v2.1 total AF is 0.000399533 (113/282,830 alleles). Both exceed the supplied PM2 maximum of 0.0001, even though the grpmax FAF values are lower; therefore the variant is not absent or sufficiently rare for PM2 under this case's generic rule.
PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)
PP5 is not met under the specified generic rule. The exact ClinVar record NM_000049.4(ASPA):c.854A>C (p.Glu285Ala) has Pathogenic and Likely pathogenic submissions, but ClinVar reports zero expert-panel submissions; the record consists of ordinary laboratory, OMIM, and other non-expert assertions. Such submissions cannot trigger PP5 here, regardless of their classifications or cited publications.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BA1 is not met. No governing VCEP-specific population source applies, so the combined all-comers gnomAD data are used. The filtering frequency required for BA1 is the grpmax FAF, not the Ashkenazi Jewish popmax point estimate: gnomAD v4.1 reports grpmax FAF = 2.585e-05 (0.002585%), far below the generic stand-alone threshold of 0.05 (5%). The Ashkenazi Jewish population has 274/29,602 observed alleles, exceeding the 2,000-allele minimum, but its popmax AF of 0.009256 is not the qualifying figure under the supplied rule. gnomAD v2.1 is concordant, with grpmax FAF = 2.293e-05.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
BS1 is not met. Canavan disease due to biallelic ASPA variants is an early-onset autosomal-recessive disorder, and this established founder allele's elevated Ashkenazi Jewish point estimate should not be treated as pathogenicity-excluding population evidence by default. Applying the supplied filtering-frequency rule, gnomAD v4.1 grpmax FAF is 2.585e-05 (0.002585%), well below the generic BS1 threshold of 0.01 (1%); gnomAD v2.1 is similarly low at 2.293e-05. The Ashkenazi Jewish popmax point estimate of approximately 0.9256% is not used for BS1, and the qualifying population has more than 2,000 observed alleles.
BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)
BS2 is not met. The governing definition requires observation in a healthy adult as a homozygote for a recessive disorder. gnomAD v4.1 reports zero homozygotes among 1,614,100 alleles, and gnomAD v2.1 reports zero homozygotes among 282,830 alleles; therefore the available population data provide no qualifying healthy-adult homozygote observation.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
BS3 is not met. The available variant-specific biochemical study does not show a lack of damaging effect; it shows the opposite. Purified E285A ASPA had only 0.3% of native enzyme activity (0.02 U/mg versus the native comparator) and reduced thermal and conformational stability. Therefore, the functional evidence is incompatible with a well-established benign functional result for this variant. No separate assay demonstrating normal protein function or normal splicing was identified.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The available evidence does not support a primarily truncating ASPA disease spectrum. PMID:16854607 states that E285A and Y231X together account for 97% of mutant alleles in the Ashkenazi Jewish population, and E285A is a missense founder variant; PMID:22850825 likewise identifies E285A as the most common Canavan-disease point mutation. This established, highly recurrent missense disease mechanism contradicts the gene-level premise required for BP1.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 is not met. The available phase observation is compound heterozygosity with IVS4+1G>T in an affected patient with autosomal recessive Canavan disease. BP2's trans branch is limited to a fully penetrant dominant gene/disorder, so this recessive trans observation does not qualify; no observation of c.854A>C in cis with a pathogenic variant is reported.
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
NM_000049.4:c.854A>C is a missense variant, p.(Glu285Ala), so the governing generic rule selects the missense REVEL path only. The REVEL score is 0.946, which does not meet any supplied BP4 threshold, including the strong threshold of <= 0.016; therefore BP4 is not met. The SpliceAI max delta of 0.054 is not substituted for REVEL because splice prediction is not the applicable path for a missense variant, and BayesDel is not usable for generic PP3/BP4.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... BP4 (strong): <= 0.016 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BP6 is not met under the specified generic rule. The exact ClinVar record has no expert-panel submission and no exact-variant ClinVar expert-panel classification of Benign or Likely benign. The available laboratory and literature assertions are pathogenic or likely pathogenic and cannot trigger BP6.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The variant is NP_000040.1:p.(Glu285Ala) from NM_000049.4:c.854A>C, and p.Glu285Ala is established as a pathogenic Canavan-disease variant. However, the available evidence does not document a previously established pathogenic alternate nucleotide change that produces the same Glu285Ala amino-acid change; the reported observations use the queried c.854A>C allele. The same-amino-acid criterion therefore cannot be established under PS1.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
No case-level evidence documents that NM_000049.4:c.854A>C arose de novo with both maternity and paternity confirmed. The available literature reports affected individuals carrying E285A, but does not provide parental testing or establish absence of a family history for this proband. Therefore, the PS2 requirements cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
ASPA has no VCEP-specific domain table. PMID:8252036's abstract states that p.Glu285Ala is predicted to be part of the aspartoacylase catalytic domain, which supports a possible critical-domain route. The available evidence does not establish that the relevant domain is without benign variation, so the complete generic PM1 requirement cannot be confirmed.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
The queried variant is p.Glu285Ala. The available PM5 comparator record contains zero candidates and zero same-residue candidates, and the reviewed literature does not document a different missense substitution at Glu285 that was determined to be pathogenic. The classic same-residue PM5 requirement therefore cannot be assessed as met.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
No case-level evidence documents an assumed de novo occurrence of NM_000049.4:c.854A>C in a patient with Canavan disease. The available literature reports affected carriers but does not establish a de novo event or provide the parental-origin information needed to apply PM6.
Assumed de novo, but without confirmation of paternity and maternity.
The available evidence does not document cosegregation of NM_000049.4:c.854A>C with disease across multiple affected family members. PMID:16854607 reports E285A in patients from unrelated families, including a homozygous patient and a compound-heterozygous patient, but does not provide informative family pedigrees, affected relatives, or segregation results. The evidence is therefore insufficient to assess PP1.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
ASPA has recurrent pathogenic missense variation, including p.Glu285Ala, and the enzyme has a loss-of-function disease mechanism. However, the available evidence does not establish both required gene-level properties: a low rate of benign missense variation and missense variants as a common mechanism of disease. No validated gene-wide missense constraint or mechanism assessment is available.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The governing definition requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. The available case material establishes the ASPA/Canavan disease context but does not provide this patient's detailed phenotype or family history sufficient to assess phenotypic specificity.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
No family-level evidence identifies an affected relative who lacks NM_000049.4:c.854A>C, and no informative non-segregation analysis is provided. The available reports do not establish a family in which affected members were tested for this variant, so BS4 cannot be assessed.
Lack of segregation in affected members of a family.
The governing definition requires the variant to be found in a case with an alternate molecular basis for disease. The available evidence reports Canavan disease cases and population controls but does not document an alternate molecular diagnosis in a case carrying c.854A>C.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_000049.4:c.854A>C in ASPA is a missense substitution predicted to produce NP_000040.1:p.(Glu285Ala). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for ASPA, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_000049.4:c.854A>C in ASPA is a missense substitution predicted to produce NP_000040.1:p.(Glu285Ala). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for ASPA, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_000049.4:c.854A>C in ASPA is a missense substitution predicted to produce NP_000040.1:p.(Glu285Ala). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for ASPA, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000049.4:c.854A>C in ASPA is a missense substitution predicted to produce NP_000040.1:p.(Glu285Ala). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for ASPA, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in ASPA, mapped onto the exon structure of NM_000049.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Ashkenazi Jewish274 / 29,602 | 0.0093 |
| Remaining individuals39 / 62,486 | 0.00062 |
| European (non-Finnish)41 / 1,180,040 | 3.5e-05 |
| Admixed American1 / 60,012 | 1.7e-05 |
| African/African American1 / 74,932 | 1.3e-05 |
| Ashkenazi Jewish96 / 10,370 | 0.0093 |
| Remaining individuals7 / 7,228 | 0.00097 |
| African/African American2 / 24,964 | 8e-05 |
| European (non-Finnish)8 / 129,156 | 6.2e-05 |
This variant is present in gnomAD v4.1 (AF= 0.000220556; MAF= 0.02206%, 356/1614100 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00925613; MAF= 0.92561%, 274/29602 alleles, homozygotes = 0); grpmax FAF= 2.585e-05.
This variant is present in gnomAD v2.1 (AF= 0.000399533; MAF= 0.03995%, 113/282830 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00925747; MAF= 0.92575%, 96/10370 alleles, homozygotes = 0); grpmax FAF= 2.293e-05.
Not available in gnomAD-Canada v1.0.
NM_000049.4:c.854A>C is a missense variant, p.(Glu285Ala), so the governing generic rule selects the missense REVEL path only. The REVEL score is 0.946, which meets the supplied PP3 strong threshold of >= 0.932 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997). The SpliceAI max delta of 0.054 is not used for PP3 because splice prediction is not the applicable path for a missense variant, and the BayesDel score is not usable because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (strong): >= 0.932 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
NM_000049.4:c.854A>C is a missense variant, p.(Glu285Ala), so the governing generic rule selects the missense REVEL path only. The REVEL score is 0.946, which does not meet any supplied BP4 threshold, including the strong threshold of <= 0.016; therefore BP4 is not met. The SpliceAI max delta of 0.054 is not substituted for REVEL because splice prediction is not the applicable path for a missense variant, and BayesDel is not usable for generic PP3/BP4.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... BP4 (strong): <= 0.016 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000049.4:c.854A>C in ASPA is a missense substitution predicted to produce NP_000040.1:p.(Glu285Ala). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for ASPA, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.946. BayesDel score = 0.575977.
12 paper records listed. 2 cited in the classification.
Nearly all (97%) of the mutant alleles in this population are due to two founder mutations, E285A and Y231X [5,10,12].
Location Introduction, paragraph 2; Table 1, patients 16 and 22
Context Mutation analysis of ASPA in 24 non-Jewish patients with Canavan disease from 23 unrelated families, using targeted testing for common mutations, sequencing, and confirmatory restriction analysis.
The point mutation that is most commonly found in CD patients (E285A) leads to a mutant aspartoacylase with the lowest activity found among the enzymes that were examined.
Location Table 1; Results and discussion, “Aspartoacylase clinical mutant activities”
Context Purified human ASPA clinical mutant expressed in Pichia pastoris; catalytic activity measured using a coupled enzyme assay.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.000220556; MAF= 0.02206%, 356/1614100 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00925613; MAF= 0.92561%, 274/29602 alleles, homozygotes = 0); grpmax FAF= 2.585e-05.
This variant is present in gnomAD v2.1 (AF= 0.000399533; MAF= 0.03995%, 113/282830 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00925747; MAF= 0.92575%, 96/10370 alleles, homozygotes = 0); grpmax FAF= 2.293e-05.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (19 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 2605)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.946. BayesDel score = 0.575977.
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV99036550, n = 1 times).
This variant does not lie in a statistically significant hotspot.