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NM_000026.4(ADSL):c.1277G>A (p.Arg426His) AND Adenylosuccinate lyase deficiency

Germline classification:
Pathogenic (9 submissions)
Last evaluated:
Jan 23, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000002566.38

Allele description [Variation Report for NM_000026.4(ADSL):c.1277G>A (p.Arg426His)]

NM_000026.4(ADSL):c.1277G>A (p.Arg426His)

Gene:
ADSL:adenylosuccinate lyase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.1
Genomic location:
Preferred name:
NM_000026.4(ADSL):c.1277G>A (p.Arg426His)
Other names:
p.R426H:CGT>CAT
HGVS:
  • NC_000022.11:g.40364965G>A
  • NG_007993.2:g.23466G>A
  • NM_000026.4:c.1277G>AMANE SELECT
  • NM_001123378.3:c.1191+600G>A
  • NM_001317923.2:c.1085G>A
  • NM_001363840.3:c.1277G>A
  • NP_000017.1:p.Arg426His
  • NP_001304852.1:p.Arg362His
  • NP_001350769.1:p.Arg426His
  • NC_000022.10:g.40760969G>A
  • NM_000026.2:c.1277G>A
  • NM_000026.3:c.1277G>A
  • NR_134256.2:n.1367G>A
  • P30566:p.Arg426His
Protein change:
R362H; ARG426HIS
Links:
UniProtKB: P30566#VAR_007978; OMIM: 608222.0002; dbSNP: rs119450941
NCBI 1000 Genomes Browser:
rs119450941
Molecular consequence:
  • NM_001123378.3:c.1191+600G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000026.4:c.1277G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317923.2:c.1085G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363840.3:c.1277G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134256.2:n.1367G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Adenylosuccinate lyase deficiency (ADSLD)
Identifiers:
MONDO: MONDO:0007068; MedGen: C0268126; Orphanet: 46; OMIM: 103050

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022724OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 2008)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV000236505Courtagen Diagnostics Laboratory, Courtagen Life Sciences
criteria provided, single submitter

(Courtagen Life Sciences Classifications)
Pathogenic
(Dec 28, 2013)
germlineclinical testing

Citation Link,

SCV000246324Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 16, 2014)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000438687Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Apr 27, 2017)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link,

SCV000631362Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 23, 2024)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

SCV000713087Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Pathogenic
(Sep 12, 2017)
germlineclinical testing

PubMed (13)
[See all records that cite these PMIDs]

SCV000894269Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 31, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001440379Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 14, 2023)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002023025Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 14, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing, literature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Adenylosuccinase deficiency presenting with epilepsy in early infancy.

Maaswinkel-Mooij PD, Laan LA, Onkenhout W, Brouwer OF, Jaeken J, Poorthuis BJ.

J Inherit Metab Dis. 1997 Aug;20(4):606-7. No abstract available.

PubMed [citation]
PMID:
9266401

Adenylosuccinate lyase deficiency.

Spiegel EK, Colman RF, Patterson D.

Mol Genet Metab. 2006 Sep-Oct;89(1-2):19-31. Epub 2006 Jul 12. Review.

PubMed [citation]
PMID:
16839792
See all PubMed Citations (18)
PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]
PMCID:
PMC4544753
PMID:
25741868
DOI:
10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000022724.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)

Description

In an infant in which epilepsy was the first manifestation of adenylosuccinase deficiency (ADSLD; 103050), Maaswinkel-Mooij et al. (1997) reported homozygosity for an arg401-to-his (R401H) substitution in the ADSL gene.

Marie et al. (1999) found 5 apparently unrelated patients with adenylosuccinate lyase deficiency who had an arg426-to-his (R426H) mutation, which had previously been identified as R401H by Maaswinkel-Mooij et al. (1997). The discrepancy in the numbering system was due to the finding by Marie et al. (1999) that the cDNA of human ADSL encodes a protein of 484 rather than 459 amino acids. The authors noted that 426H mutation was the most frequent one identified to that time, accounting for 12 of the 34 alleles investigated.

Kmoch et al. (2000) described a patient with ADSLD who was homozygous for the R426H mutation.

Edery et al. (2003) observed an unusually variable combination of clinical features and striking intrafamilial variability in the phenotype. Among 3 sibs from a family originally from Portugal, the proband had marked psychomotor regression and progressive cerebellar vermis atrophy; the other 2 affected sibs presented mainly autistic features. The sibs were homozygous for the R426H mutation. The authors suggested that, in any patient with mental retardation of unexplained origin, adenylosuccinate lyase deficiency should be considered and assessed using a simple urinary screening method for the presence of succinylpurines.

Jurecka et al. (2008) identified homozygosity for the R426H mutation in 2 unrelated Polish patients with ADSL deficiency. One had a severe form of the disorder with severe psychomotor retardation, inability to walk, and refractory seizures, and was bedridden by age 9.5. The other had a relatively less severe phenotype and could sit and walk a few steps at age 4.5 years. Two additional unrelated Polish patients were compound heterozygous for the R426H allele and another pathogenic mutation in the ADSL gene.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Courtagen Diagnostics Laboratory, Courtagen Life Sciences, SCV000236505.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000246324.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000438687.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

The ADSL c.1277G>A (p.Arg426His) variant has been identified in a homozygous state in 13 individuals with adenylosuccinase deficiency, in a compound heterozygous state in four individuals, and in a heterozygous state in six unaffected family members (Marie et al. 1999; Kmoch et al. 2000; Edery et al. 2003; Jurecka et al. 2008; Donti et al. 2016). The p.Arg426His variant was absent from 88 controls and is reported at a frequency of 0.00042 in the European (non-Finnish) population of the Exome Aggregation Consortium. In vitro functional studies demonstrated that the p.Arg426His mutant enzyme resulted in approximately 50% of wild type activity. Biochemical analyses showed that the p.Arg426His variant produced an unstable protein (Kmoch et al. 2000; Jurecka et al. 2008; Zikanova et al. 2010). Based on the collective evidence, the p.Arg426His variant is classified as pathogenic for adenylosuccinase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000631362.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 426 of the ADSL protein (p.Arg426His). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individuals with adenylosuccinate lyase deficiency (PMID: 10090474, 12833398, 16839792, 18524658, 25112391, 27504266). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2462). 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 ADSL protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ADSL function (PMID: 18524658, 20127976). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000713087.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (13)

Description

The p.Arg426His (NM_000026.2 c.1277G>A) variant in ADSL has been reported in 11 homozygotes and 9 compound heterozygous individuals with Adenylosuccinate lyase deficiency (ADSL) (Cantwell 1988, Marie 1999, Kmoch 2000, Mouchegh 2007, Jurecka 2008, Lundy 2010, Henneke 2010, Jurecka 2016 and Donti 2016), and segregated in 3 family members in 2 families (Edery 2003 Donti 2016), and has been reported i n ClinVar (Variation ID#2462) by multiple laboratories as pathogenic. In vitro f unctional studies provide evidence supporting an impact on protein function (Bar esova 2012 and Zikanova 2010). This variant has been identified in 0.042% (28/66 ,740) of European chromosomes by the Exome Aggregation Consortium (ExAC, http:// exac.broadinstitute.org; dbSNP rs119450941). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In summary, this variant meets criteria to be class ified as pathogenic for ADSL in an autosomal recessive manner based upon biallel ic case observations, segregation in affected individuals and functional evidenc e.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

From Fulgent Genetics, Fulgent Genetics, SCV000894269.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440379.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria applied: PM3_VSTR,PM5,PM2_SUP,PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002023025.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024