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NM_000454.5(SOD1):c.272A>C (p.Asp91Ala) AND Amyotrophic lateral sclerosis type 1

Germline classification:
Conflicting interpretations of pathogenicity (9 submissions)
Last evaluated:
Mar 6, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000015888.47

Allele description [Variation Report for NM_000454.5(SOD1):c.272A>C (p.Asp91Ala)]

NM_000454.5(SOD1):c.272A>C (p.Asp91Ala)

Gene:
SOD1:superoxide dismutase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.11
Genomic location:
Preferred name:
NM_000454.5(SOD1):c.272A>C (p.Asp91Ala)
Other names:
D90A
HGVS:
  • NC_000021.9:g.31667290A>C
  • NG_008689.1:g.12669A>C
  • NM_000454.5:c.272A>CMANE SELECT
  • NP_000445.1:p.Asp91Ala
  • NP_000445.1:p.Asp91Ala
  • LRG_652t1:c.272A>C
  • LRG_652:g.12669A>C
  • LRG_652p1:p.Asp91Ala
  • NC_000021.8:g.33039603A>C
  • NM_000454.4:c.272A>C
  • P00441:p.Asp91Ala
Protein change:
D91A; ASP90ALA
Links:
UniProtKB: P00441#VAR_007145; OMIM: 147450.0015; dbSNP: rs80265967
NCBI 1000 Genomes Browser:
rs80265967
Molecular consequence:
  • NM_000454.5:c.272A>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
10

Condition(s)

Name:
Amyotrophic lateral sclerosis type 1 (ALS1)
Synonyms:
AMYOTROPHIC LATERAL SCLEROSIS 1, FAMILIAL
Identifiers:
MONDO: MONDO:0007103; MedGen: C1862939; Orphanet: 803; OMIM: 105400

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000036155OMIM
no assertion criteria provided
Pathogenic
(Apr 10, 2007)
germlineliterature only

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

SCV000597223Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Dec 12, 2016)
germlineclinical testing

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

SCV000766153Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Dec 18, 2023)
germlineclinical testing

PubMed (24)
[See all records that cite these PMIDs]

SCV000787782Institute of Human Genetics, Cologne University
no assertion criteria provided
Pathogenic
(Apr 25, 2018)
germlineclinical testing

SCV001141287Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Pathogenic
(Mar 30, 2023)
unknownclinical testing

Citation Link,

SCV001251054Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 31, 2020)
germlineresearch

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

SCV002580444MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Sep 13, 2021)
germlineclinical testing

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

SCV0038418013billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Feb 23, 2023)
unknownclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV005040188Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Mar 6, 2024)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes10not providednot providednot providednot providedclinical testing, research
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutational analysis of the Cu/Zn superoxide dismutase gene in 23 familial and 69 sporadic cases of amyotrophic lateral sclerosis in Belgium.

Aguirre T, Matthijs G, Robberecht W, Tilkin P, Cassiman JJ.

Eur J Hum Genet. 1999 Jul;7(5):599-602.

PubMed [citation]
PMID:
10439968

Compound heterozygous D90A and D96N SOD1 mutations in a recessive amyotrophic lateral sclerosis family.

Hand CK, Mayeux-Portas V, Khoris J, Briolotti V, Clavelou P, Camu W, Rouleau GA.

Ann Neurol. 2001 Feb;49(2):267-71.

PubMed [citation]
PMID:
11220750
See all PubMed Citations (32)

Details of each submission

From OMIM, SCV000036155.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (8)

Description

In 14 affected individuals from 4 unrelated Swedish or Finnish families with ALS (105400), Andersen et al. (1995) identified a homozygous mutation in exon 4 of the SOD1 gene, resulting in an asp90-to-ala (D90A) substitution. Erythrocyte SOD1 activity was essentially normal. The findings suggested that this mutation caused ALS by a gain of function rather than by loss, and that the D90A mutation was less detrimental than previously reported mutations. Consanguinity was present in several of the families. The age at onset of symptoms ranged from 37 to 94 years in 1 family in which all patients showed very similar disease phenotypes; symptoms began with cramps in the legs, which progressed to muscular atrophy and weakness. Upper motor neuron signs appeared after 1-4 years disease duration in all patients; none of the patients showed signs of intellectual impairment. In a second family, onset in 2 sibs was at the age of 40, with a phenotype similar to that of the first family. In a third family, 3 sibs had onset at ages 20, 36, and 22 years, respectively. Four patients with apparently sporadic ALS were also found to carry the mutations. Andersen et al. (1995) concluded that familial ALS due to mutation in the SOD1 gene exists in both autosomal dominant and autosomal recessive forms.

Robberecht et al. (1996) identified a heterozygous D90A mutation in affected members of 2 families with ALS and in a patient with apparently sporadic ALS. Aguirre et al. (1999) found the D90A mutation in heterozygous state in affected members of 2 families and in 1 apparently sporadic case of ALS. Direct sequencing of exons 1 through 5 showed no additional mutations in the SOD1 gene in these patients and the D90A mutation was not found on 150 normal chromosomes.

In a worldwide haplotype study of 28 pedigrees with the D90A mutation, Al-Chalabi et al. (1998) found that 20 recessive families shared the same founder haplotype, regardless of geographic location, whereas several founders existed for the 8 dominant families. The findings confirmed that D90A can act in a dominant fashion in keeping with all other SOD1 mutations. Al-Chalabi et al. (1998) proposed that a tightly linked protective factor modifies the toxic effect of mutant SOD1 in recessive families.

Gellera et al. (2001) found homozygosity for the D90A mutation in a sporadic case of ALS.

In 2 sibs with ALS from a family described by Khoris et al. (2000), Hand et al. (2001) identified compound heterozygosity for D90A and D96N (147450.0032). A third sib with the disease died before testing. Further examination of the family identified the D90A mutation alone in 2 unaffected members and the D96N mutation alone in 4 unaffected members. There were no individuals homozygous for either mutation, and no unaffected individual with both mutations was identified. Hand et al. (2001) concluded that both mutations, which occur in the same region of the protein, are required for disease. The authors emphasized that this is the first report of compound heterozygosity for the SOD1 gene in an ALS patient and suggested that the findings may have implications for the interpretation of inheritance patterns in ALS families.

Using PET scanning, Turner et al. (2007) found that ALS patients homozygous for the D90A substitution had a 12% decrease in 5-HT1A receptor (5HTRA1; 109760) binding potential compared to healthy controls. The decreased binding among patients was most significant in the temporal lobes. Patients with sporadic ALS without the D90A substitution had a 21% decrease in binding potential. Turner et al. (2007) suggested that patients with the D90A mutation may have decreased cortical vulnerability compared to other ALS patients, which may correlate with the slower progression observed in D90A carriers.

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

From Genetic Services Laboratory, University of Chicago, SCV000597223.1

#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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000766153.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (24)

Description

This sequence change replaces aspartic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 91 of the SOD1 protein (p.Asp91Ala). This variant is present in population databases (rs80265967, gnomAD 1.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with autosomal recessive amyotrophic lateral sclerosis (PMID: 7647793, 10809943, 11220750, 11284995, 11369193, 14506936, 18608106, 19703565, 20460594, 22264771, 23062701, 23280792). This variant has been reported in individual(s) with autosomal dominant amyotrophic lateral sclerosis (PMID: 8909456, 10809943, 14506936, 19922148, 22264771); however, the role of the variant in this condition is currently unclear. This variant is also known as p.Asp90Ala. ClinVar contains an entry for this variant (Variation ID: 14766). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Experimental studies have shown that this missense change affects SOD1 function (PMID: 7655469, 12482932, 16945901, 17420412, 18319614, 19635794, 19703565, 20189984, 22264771, 25509359, 25792239). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From Institute of Human Genetics, Cologne University, SCV000787782.1

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

From Mendelics, SCV001141287.2

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

From Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University, SCV001251054.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided9not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided9not providednot providednot provided

From MGZ Medical Genetics Center, SCV002580444.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From 3billion, SCV003841801.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.150%). The variant is observed as homozygous in at least two unrelated individuals/adults in the gnomAD v.2.1.1 dataset. The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (3Cnet: 0.84). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with SOD1 related disorder (ClinVar ID: VCV000014766 / PMID: 7647793). Different missense changes at the same codon (p.Asp91Asn, p.Asp91Val) have been reported to be associated with SOD1 related disorder (PMID: 22632444). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005040188.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

Variant summary: SOD1 c.272A>C (p.Asp91Ala), also referred to as p.D90A in the literature, results in a non-conservative amino acid change located in the superoxide dismutase, copper/zinc binding domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0014 in 251472 control chromosomes in the gnomAD database, including 2 homozygotes. c.272A>C has been reported in the literature in multiple homozygous individuals affected with Amyotrophic Lateral Sclerosis (ALS) from families where the disorder is inherited in an autosomal recessive pattern, the majority of whom are of Scandinavian ancestry. Although the variant has been found to segregate with ALS in several of these families (e.g. Anderson_1995), there are also kindreds where the variant is only found in affected individuals from one branch of the family, while affected individuals from another branch do not have the variant (e.g. Felbecker_2010). Additionally, unaffected homozygous individuals have been reported in at least one family, suggesting reduced penetrance (e.g. Khoris_2000). The variant has also been reported in the heterozygous state in multiple individuals with autosomal dominant ALS (e.g. Robberecht_1996, Khoris_2000, Berdynski_2022). It has been found that families with autosomal recessive inheritance share the same founder haplotype, whereas several founders exist for those with the variant who exhibit an autosomal dominant pattern of inheritance (Al-Chalabi_1998). Altogether, these data indicate that the variant is likely to be associated with disease. Several publications report experimental evidence evaluating an impact on protein function (e.g. Anderson_1995, Lindberg_2002, Jonsson_2002, Prudencio_2009, Chen_2023). While the variant does not appear to negatively affect Cu-Zn-SOD activity, in at least two studies it has been found to result in significantly increased protein aggregation compared to the wild type protein (e.g. Prudencio_2009, Chen_2023). The following publications have been ascertained in the context of this evaluation (PMID: 9817920, 7647793, 34996976, 36376198, 20460594, 12270693, 10809943, 12482932, 19483195, 8909456). ClinVar contains an entry for this variant (Variation ID: 14766). Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Oct 20, 2024