rs142073798
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Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PP3PP5_Very_Strong
The NM_213599.3(ANO5):c.2498T>A(p.Met833Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,610,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000098 ( 0 hom. )
Consequence
ANO5
NM_213599.3 missense
NM_213599.3 missense
Scores
10
7
2
Clinical Significance
Conservation
PhyloP100: 7.95
Genes affected
ANO5 (HGNC:27337): (anoctamin 5) This gene encodes a member of the anoctamin family of transmembrane proteins. The encoded protein is likely a calcium activated chloride channel. Mutations in this gene have been associated with gnathodiaphyseal dysplasia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.809
PP5
Variant 11-22276177-T-A is Pathogenic according to our data. Variant chr11-22276177-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 285338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-22276177-T-A is described in Lovd as [Likely_pathogenic]. Variant chr11-22276177-T-A is described in Lovd as [Pathogenic]. Variant chr11-22276177-T-A is described in Lovd as [Pathogenic]. Variant chr11-22276177-T-A is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 151824Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000120 AC: 30AN: 250750Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135564
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GnomAD4 exome AF: 0.0000980 AC: 143AN: 1458828Hom.: 0 Cov.: 31 AF XY: 0.0000951 AC XY: 69AN XY: 725810
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GnomAD4 genome AF: 0.000132 AC: 20AN: 151824Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74174
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:5
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 27, 2017 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 18, 2022 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23663589, 25891276, 23607914, 30919934, 32528171, 29431110, 34426522, 34008892) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 11, 2024 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 27, 2023 | The frequency of this variant in the general population is consistent with pathogenicity. (http://gnomad.broadinstitute.org) This variant has been identified in multiple unrelated individuals with autosomal recessive limb-girdle muscular dystrophy. Computational tools predict that this variant is damaging. - |
ANO5-related disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Aug 16, 2018 | The ANO5 c.2498T>A (p.Met833Lys) missense variant has been reported in three studies in which it is found in three unrelated individuals affected with muscular dystrophy who had high levels of creatine kinase, including one who carried the variant in a homozygous state and two who carried the variant in a compound heterozygous state with known or suspected null variants in trans (van der Kooi et al. 2013; Liewluck et al. 2013; Savarese et al. 2015). The p.Met833Lys variant was absent from 52 control individuals (Savarese et al. 2015) and present in a heterozygous state in three unaffected first-degree relatives of probands (van der Kooi et al. 2013; Liewluck et al. 2013). The p.Met833Lys variant is reported at a frequency of 0.001085 in the Ashkenazi Jewish population of the Genome Aggregation Database. Based on the combined clinical evidence, the p.Met833Lys variant is classified as likely pathogenic for ANO5-Related Disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
Gnathodiaphyseal dysplasia;C1969785:Autosomal recessive limb-girdle muscular dystrophy type 2L;C2750076:Miyoshi muscular dystrophy 3 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 27, 2022 | - - |
Gnathodiaphyseal dysplasia;C1969785:Autosomal recessive limb-girdle muscular dystrophy type 2L Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 10, 2024 | This sequence change replaces methionine, which is neutral and non-polar, with lysine, which is basic and polar, at codon 833 of the ANO5 protein (p.Met833Lys). This variant is present in population databases (rs142073798, gnomAD 0.1%). This missense change has been observed in individual(s) with limb girdle or distal muscular dystrophy (PMID: 23607914, 23663589, 25891276). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 285338). 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 ANO5 protein function with a positive predictive value of 80%. This variant disrupts the p.Met833 amino acid residue in ANO5. Other variant(s) that disrupt this residue have been observed in individuals with ANO5-related conditions (PMID: 31350120), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. - |
Autosomal recessive limb-girdle muscular dystrophy type 2L Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | Oct 01, 2021 | PM3, PP2, PP3, PP5, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
P
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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