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NM_213599.3(ANO5):c.2272C>T (p.Arg758Cys) AND Autosomal recessive limb-girdle muscular dystrophy type 2L

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Mar 30, 2023
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:
RCV000032966.15

Allele description [Variation Report for NM_213599.3(ANO5):c.2272C>T (p.Arg758Cys)]

NM_213599.3(ANO5):c.2272C>T (p.Arg758Cys)

Gene:
ANO5:anoctamin 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p14.3
Genomic location:
Preferred name:
NM_213599.3(ANO5):c.2272C>T (p.Arg758Cys)
HGVS:
  • NC_000011.10:g.22274605C>T
  • NG_015844.1:g.86430C>T
  • NM_001142649.2:c.2269C>T
  • NM_213599.3:c.2272C>TMANE SELECT
  • NP_001136121.1:p.Arg757Cys
  • NP_998764.1:p.Arg758Cys
  • NP_998764.1:p.Arg758Cys
  • LRG_868t1:c.2272C>T
  • LRG_868:g.86430C>T
  • LRG_868p1:p.Arg758Cys
  • NC_000011.9:g.22296151C>T
  • NM_213599.2:c.2272C>T
  • Q75V66:p.Arg758Cys
  • p.(Arg758Cys)
Protein change:
R757C; ARG758CYS
Links:
UniProtKB: Q75V66#VAR_063583; OMIM: 608662.0006; dbSNP: rs137854529
NCBI 1000 Genomes Browser:
rs137854529
Molecular consequence:
  • NM_001142649.2:c.2269C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_213599.3:c.2272C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2L (LGMDR12)
Synonyms:
Limb-girdle muscular dystrophy, type 2L; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 12
Identifiers:
MONDO: MONDO:0012652; MedGen: C1969785; Orphanet: 206549; OMIM: 611307

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000245577Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq
criteria provided, single submitter

(LMM Criteria)
Pathogenic
(Jul 28, 2014)
germlineclinical testing

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

SCV000809057OMIM
no assertion criteria provided
Pathogenic
(Mar 20, 2012)
germlineliterature only

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

SCV001164480Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 3, 2018)
germlineresearch

PubMed (7)
[See all records that cite these PMIDs]

SCV002503759Molecular Genetics, Royal Melbourne Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 30, 2023)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV002581057MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 25, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing, research
not providedgermlinenot provided11not providednot providednot providedliterature only, clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Patients with a non-dysferlin Miyoshi myopathy have a novel membrane repair defect.

Jaiswal JK, Marlow G, Summerill G, Mahjneh I, Mueller S, Hill M, Miyake K, Haase H, Anderson LV, Richard I, Kiuru-Enari S, McNeil PL, Simon SM, Bashir R.

Traffic. 2007 Jan;8(1):77-88. Epub 2006 Nov 21.

PubMed [citation]
PMID:
17132147
See all PubMed Citations (9)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq, SCV000245577.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (5)

Description

The Arg758Cys variant in ANO5 has been reported in >20 homozygous and compound heterozygous individuals with muscular dystrophy and was found to segregate with disease in 3 affected relatives (Bolduc 2010, Hicks 2011, Penttila 2010, Sarkozy 2012). This variant has been identified in 1% (2/186) of Finnish chromosomes by the 1000 Genomes Project (dbSNP rs157854529) and is a known Finnish founder variant. Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational analyses (biochemical amino acid properties, conservation, PolyPhen2, and SIFT) suggest that the p.Arg758Cys variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, this variant meets our criteria to be classified as pathogenic (http://pcpgm.partners.org/LMM).

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

From OMIM, SCV000809057.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In 2 Finnish brothers with Miyoshi muscular dystrophy-3 (MMD3; 613319), Bolduc et al. (2010) identified a homozygous 2272C-T transition in exon 20 of the ANO5 gene, resulting in an arg758-to-cys (R758C) substitution in a conserved residue in an extracellular loop. The R758C variant was not detected in 100 UK or 208 French Canadian control chromosomes, but was detected in 1 of 368 Finnish control chromosomes, indicating that this variant is present in the Finnish population at a low frequency. The family had originally been reported by Jaiswal et al. (2007).

Among 25 patients, mostly of Finnish descent, with variable muscle disorders due to recessive ANO5 mutations, Penttila et al. (2012) found that R758C was the most common mutation, occurring in homozygous state in 9 Finnish patients and in heterozygous state with another pathogenic allele (see, e.g., 608662.0007 and 608662.0008) in 11 patients. The phenotype was highly variable: 2 females who were homozygous for the mutation had no clinical muscle weakness and only hyperCKemia, whereas other women with the mutation had myalgia and/or calf hypertrophy. Men with the mutation showed distal lower limb weakness or proximal upper and lower limb muscle weakness (LGMDR12; 611307). The findings indicated that this mutation can be associated with a variety of muscle phenotypes.

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

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001164480.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (7)

Description

The homozygous p.Arg758Cys variant in ANO5 was identified by our study in one individual with limb-girdle muscular dystrophy (LGMD). This variant has been identified in 0.06604% (182/275600) of chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs137854529). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The p.Arg758Cys variant in ANO5 has been reported in 26 individuals with ANO5-associated muscular dystrophy in the literature and segregated with disease in 4 affected relatives from 2 families (PMID: 27911336, 22402862, 21739273, 21186264, 20096397, 22980763). The presence of this variant in combination with 5 reported pathogenic (or likely pathogenic) variants and in 15 individuals with muscular dystrophy increases the likelihood that the p.Arg758Cys variant is pathogenic (PMID: 22980763). This variant has also been reported pathogenic in ClinVar (Variation ID: 2166). In summary, this variant meets criteria to be classified as pathogenic for LGMD in an autosomal recessive manner based on reports in ClinVar and multiple occurrences with reported pathogenic ANO5 variants in individuals with muscular dystrophy. ACMG/AMP Criteria applied: PM2, PP3, PP1_Moderate, PM3_VeryStrong (Richards 2015).

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

From Molecular Genetics, Royal Melbourne Hospital, SCV002503759.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change is predicted to replace arginine with cysteine at codon 758 of the ANO5 protein (p.(Arg758Cys)). The arginine residue is invariant across species (100 vertebrates, UCSC), and is located in the anoctamin domain. There is a large physicochemical difference between arginine and cysteine. The variant is present in a large population cohort at a frequency of 0.5% in the Finnish European population (rs137854529), and is recognised to be a Finnish founder mutation (PMID: 20096397, 22402862, 27911336; gnomAD v2.1.1 and v3.0). The frequency of the variant in the next most common population, European (non-Finnish), is 0.03%. This variant has been previously reported in affected individuals in homozygous state, and in heterozygous state along with another pathogenic variant (PM3_VeryStrong; PMID: 22402862, 21739273, 21186264, 22980763). It has been shown to segregate with disease in two affected siblings in the homozygous state (PP1; PMID: 20096397). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (PP3; 5/6 algorithms). Based on the variant classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as PATHOGENIC. The following criteria are met: PM3_VeryStrong, PP1, PP3.

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

From MGZ Medical Genetics Center, SCV002581057.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Oct 20, 2024