Submissions for variant NM_014874.4(MFN2):c.2119C>T (p.Arg707Trp)

gnomAD frequency: 0.00029  dbSNP: rs119103267

Total submissions: 27

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000199654	SCV000251722	pathogenic	not provided	2023-04-19	criteria provided, single submitter	clinical testing	R707W was identified in the homozygous state in multiple independent families with a lipodystrophic syndrome (Capel et al., 2018); 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: 28492532, 22492563, 25025039, 28251916, 26306937, 24126688, 20350294, 26085578, 26114802, 28414270, 31589614, 24957169, 24819634, 31980526, 33415332, 32376792, 29867446, 32916636, 33502018, 34426522, 29358271, 26392352, 25231362, 35641312, 20008656, 30158064, 18458227)
Invitae	RCV000472857	SCV000547929	pathogenic	Charcot-Marie-Tooth disease type 2	2024-01-31	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 707 of the MFN2 protein (p.Arg707Trp). This variant is present in population databases (rs119103267, gnomAD 0.05%). This missense change has been observed in individual(s) with Charcot-Marie-Tooth disease and/or multiple symmetric lipomatosis and neuropathy (PMID: 18458227, 20008656, 20350294, 22492563, 25025039, 26085578, 26114802, 28251916, 28414270, 30158064, 33415332). 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: 2280). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MFN2 protein function. Experimental studies have shown that this missense change affects MFN2 function (PMID: 26085578). For these reasons, this variant has been classified as Pathogenic.
Eurofins Ntd Llc (ga)	RCV000199654	SCV000705467	pathogenic	not provided	2017-01-23	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000624830	SCV000741959	pathogenic	Inborn genetic diseases	2022-11-04	criteria provided, single submitter	clinical testing	The c.2119C>T (p.R707W) alteration is located in exon 18 (coding exon 16) of the MFN2 gene. This alteration results from a C to T substitution at nucleotide position 2119, causing the arginine (R) at amino acid position 707 to be replaced by a tryptophan (W)._x000D_ _x000D_ Based on the available evidence, the MFN2 c.2119C>T (p.R707W) alteration is classified as pathogenic for autosomal recessive MFN2-related neuropathy; however, it is unlikely to be causative of autosomal dominant MFN2-related neuropathy. Based on data from gnomAD, the T allele has an overall frequency of 0.025% (71/282876) total alleles studied. The highest observed frequency was 0.051% (66/129186) of European (non-Finnish) alleles. This alteration was reported in the homozygous state or in trans with another MFN2 variant in multiple individuals with axonal neuropathy and lipodystrophy (Nicholson, 2008; Calvo, 2009; Carr, 2015; Sawyer, 2015; Rocha, 2017; Capel, 2018). Heterozygous parents with affected children have been reported to be asymptomatic (Nicholson, 2008; Carr, 2015; Rocha, 2017). This amino acid position is well conserved in available vertebrate species. Functional analysis in patient fibroblasts demonstrated that the p.R707W alteration impairs mitofusin 2 homodimer formation leading to mitochondrial aggregation (Sawyer, 2015). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
SIB Swiss Institute of Bioinformatics	RCV000002369	SCV000803475	likely pathogenic	Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;	2018-05-31	criteria provided, single submitter	curation	This variant is interpreted as a Likely Pathogenic, for Charcot-Marie-Tooth disease, axonal, type 2A2B, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PS3 => Well-established functional studies show a deleterious effect (PMID:26085578).
Fulgent Genetics, Fulgent Genetics	RCV002476912	SCV000893874	pathogenic	Charcot-Marie-Tooth disease type 2A2; Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;; Neuropathy, hereditary motor and sensory, type 6A	2022-03-22	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000778183	SCV000914347	pathogenic	MFN2-related disorder	2018-12-19	criteria provided, single submitter	clinical testing	Across a selection of the available literature, the MFN2 c.2119C>T (p.Arg707Trp) missense variant has been identified in a total of 11 individuals with MFN2-related disorders, including in a homozygous state in four individuals, (two of whom are related), in a compound heterozygous state in four individuals, and in a heterozygous state in three individuals (Nicholson et al. 2008; Calvo et al. 2009; Braathen et al. 2010; Sitarz et al. 2012; Brozkova et al. 2013; Hoyer et al. 2014; Sawyer et al. 2015; Carr et al. 2015). The variant was also found in a heterozygous state in several asymptomatic parents, consistent with an autosomal recessive pattern of inheritance. MFN2-related disorders have also been reported to follow an autosomal dominant pattern of inheritance which was observed through four generations of one family in a study by Braathen et al. (2010). The p.Arg707Trp variant was absent from at least 602 evaluated control alleles (Nicholson et al. 2008; Braathen et al. 2010) and is reported at a frequency of 0.000581 in the European American population of the Exome Sequencing Project. Functional studies in U2OS cells homozygous for the p.Arg707Trp variant demonstrate a reduced ability to form homotypic MFN2 protein interactions in vitro and to tubulate mitochondria which were more prone to aggregation (Sawyer et al. 2015). The p.Arg707Trp variant is located in a well-conserved residue in a known functional domain that is thought to permit homotypic protein interaction as well as heterotypic binding to MFN1 (Sawyer et al. 2015). Based on the collective evidence, the p.Arg707Trp variant is classified as pathogenic for MFN2-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000239892	SCV000966809	likely pathogenic	Charcot-Marie-Tooth disease type 2A2	2019-02-11	criteria provided, single submitter	clinical testing	The p.Arg707Trp variant in MFN2 has been reported in the heterozygous state in 4 probands with clinical features of Charcot-Marie-Tooth disease type 2A (CMT2A; Braathen 2010, Sitarz 2012, Brožková 2013, Bansagi 2017). It has also been reported in the compound heterozygous or homozygous state in at least 9 individuals with CMT2A-related neuropathy and lipomatosis or lipodystrophy (Nicholson 2008, Calvo 2009, Carr 2015, Sawyer 2015, Rocha 2017, Capel 2018). The variant segregated with neuropathy and lipomatosis/lipodystrophy in at least 4 affected members of 3 families (Calvo 2009, Rocha 2017, Capel 2018). This variant has also been identified in the heterozygous state in individuals without overt signs of neuropathy (Nicholson 2008, Calvo 2009, Brožková 2013, Carr 2015, Rocha 2017) and in 0.05% (66/129186) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). However, this is consistent with the fact that variable expressivity including sub-clinical, late-onset neuropathy has been reported for CMT2A (Züchner 2013). Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Furthermore, analysis of patient fibroblasts suggest that the p.Arg707Trp variant may impair mitochondrial function (Sawyer 2015). In summary, although additional studies are required to fully establish its clinical significance, the p.Arg707Trp variant meets criteria to be classified as likely pathogenic for autosomal dominant CMT2A, with homozygous or compound heteroygous occurences likely leading to a more severe course of disease that may include lipomatosis and/or lipodystrophy. ACMG/AMP Criteria applied: PM3_Strong, PP3, PS3_Supporting, PS4_Supporting.
Molecular Genetics Laboratory, London Health Sciences Centre	RCV001173687	SCV001336791	pathogenic	Charcot-Marie-Tooth disease		criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000239892	SCV001524155	pathogenic	Charcot-Marie-Tooth disease type 2A2	2019-04-12	criteria provided, single submitter	clinical testing	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
CeGaT Center for Human Genetics Tuebingen	RCV000199654	SCV001961079	pathogenic	not provided	2024-04-01	criteria provided, single submitter	clinical testing	MFN2: PM3:Very Strong, PM2:Supporting, PM5:Supporting, PP1, PS3:Supporting
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV001775061	SCV002012458	pathogenic	Peripheral axonal neuropathy	2019-12-25	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000199654	SCV002024345	pathogenic	not provided	2021-08-13	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000778183	SCV002500234	pathogenic	MFN2-related disorder	2022-03-08	criteria provided, single submitter	clinical testing	Variant summary: MFN2 c.2119C>T (p.Arg707Trp) results in a non-conservative amino acid change located in the Fzo/mitofusin HR2 domain (IPR006884) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00025 in 251494 control chromosomes (gnomAD). c.2119C>T has been reported in the literature in multiple individuals affected with MFN2-Related Disorders, including one homozygote diagnosed with severe early onset axonal neuropathy (e.g. Nicholson_2008), and several compound heterozygotes diagnosed with Charcot-Marie-Tooth disease (e.g. Calvo_2009, Brozkova_2013, Pipis_2020). These data indicate that the variant is very likely to be associated with disease and are consistent with an autosomal recessive inheritance pattern. Additionally, affected individuals (e.g. Braathen_2010) and unaffected individuals have been reportes as heterozygous carriers, therefore the relationship of this variant to autosomal dominant disease is unclear. At least one publication reports experimental evidence evaluating an impact on protein function, showing that the variant protein resulted in mitochondrial aggregation and defects in homo-oligomerization (Sawyer_2015). Twelve ClinVar submitters have assessed the variant since 2014: four classified the variant as likely pathogenic, and eight as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Mendelics	RCV002247240	SCV002517612	pathogenic	Neuropathy, hereditary motor and sensory, type 6A	2022-05-04	criteria provided, single submitter	clinical testing
3billion	RCV000002369	SCV002521820	likely pathogenic	Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;	2022-05-22	criteria provided, single submitter	clinical testing	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.025%). Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.84; 3Cnet: 0.86). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000002280). A different missense change at the same codon (p.Arg707Pro) has been reported to be associated with MFN2 related disorder (ClinVar ID: VCV000637750 / PMID: 22492563). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	RCV002285136	SCV002575022	likely pathogenic	Charcot-Marie-Tooth disease type 2A2; Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;	2022-09-26	criteria provided, single submitter	research	PS3_Moderate, PS4_Moderate (for AD CMT) or PM3_Strong (for AR CMT), PP1, PP3
Institute of Human Genetics, University of Leipzig Medical Center	RCV000002369	SCV003804736	pathogenic	Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;	2023-01-30	criteria provided, single submitter	clinical testing	_x000D_This variant was identified together with NM_014874.4:c.1160+1G>A. Criteria applied: PM3_VSTR, PS3_SUP, PP3
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	RCV002476912	SCV003920211	pathogenic	Charcot-Marie-Tooth disease type 2A2; Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;; Neuropathy, hereditary motor and sensory, type 6A	2021-03-30	criteria provided, single submitter	clinical testing	MFN2 NM_014874.3 exon 18 p.Arg707Trp (c.2119C>T): This variant has been reported in the literature in the heterozygous, compound heterozygous, or homozygous state in several individuals with axonal neuropathy, segregating with at least 3 affected family members within 2 families (Nicholson 2008 PMID:18458227, Calvo 2009 PMID:20008656, Brozkova 2013 PMID:24126688, Hoyer 2014 PMID:25025039, Sawyer 2015 PMID:26085578, Bansagi 2017 PMID:28251916). This variant has also been reported in individuals with multiple symmetric lipomatosis in addition to neuropathy (Carr 2015 PMID:26114802, Sawyer 2015 PMID:26085578). This variant is present in 0.05% (66/129186) of European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/1-12069698-C-T). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population, carrier status, and/or variable expressivity. This variant is also present in ClinVar, with several labs classifying this variant as pathogenic or likely pathogenic (Variation ID:2280). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In addition, a functional study in fibroblasts has shown a deleterious effect of this variant (Sawyer 2015 PMID:26085578). However, this study may not accurately represent in vivo biological function. In summary, this variant is classified as pathogenic based on the data above.
PreventionGenetics, part of Exact Sciences	RCV000778183	SCV004113565	pathogenic	MFN2-related disorder	2024-02-20	criteria provided, single submitter	clinical testing	The MFN2 c.2119C>T variant is predicted to result in the amino acid substitution p.Arg707Trp. This variant has previously been reported in several individuals with diverse phenotypes. In an individual with severe early-onset axonal neuropathy and lipodystrophy, this variant was found in the homozygous state (Nicholson et al. 2008. PubMed ID: 18458227). In another study, six patients from five families presented with a lipodystrophy with variable Charcot-Marie-Tooth features; each of these individuals harbored the p.Arg707Trp variant in the homozygous state (Capel et al. 2018. PubMed ID: 30158064). In another family with two brothers affected with multiple symmetric lipomatosis and neuropathy, whole exome sequencing identified they were also homozygous for the c.2119C>T variant (Sawyer et al. 2015. PubMed ID: 26085578). In another family with three affected children with early-onset Charcot-Marie-Tooth disease, all were found to be compound heterozygous for the c.2119C>T variant and a second plausible causative variant (Calvo et al. 2009. PubMed ID: 20008656). Lastly, this variant was found in the compound heterozygous state with an exon 7-8 deletion in an individual with suspected Charcot-Marie-Tooth disease (Carr et al. 2015. PubMed ID: 26114802). Functional studies in fibroblasts show that the p.Arg707Trp variant impairs MFN2-MFN2 protein interactions in mitochondria, making mitochondria prone to perinuclear aggregation (Sawyer et al. 2015. PubMed ID: 26085578). In summary, this evidence suggests the c.2119C>T variant is inherited in an autosomal recessive manner and is pathogenic for disease.
Breakthrough Genomics, Breakthrough Genomics	RCV000239892	SCV005088857	likely pathogenic	Charcot-Marie-Tooth disease type 2A2	2020-10-27	criteria provided, single submitter	clinical testing	This variant has been reported in multiple individuals and families affected with Charcot Marie Tooth disease type 2 (CMT2) in the heterozygous, homozygous, or compound heterozygous state [PMID: 18458227, 24126688, 25025039, 22492563, 20008656] and also been reported to segregate with disease [PMID: 20350294, 20008656]. There have been reports of patients harboring the variant in heterozygous condition presenting with clinical features of CMT2 [PMID: 20350294] and early severe axonal CMT as well as cases with unaffected heterozygous parents [PMID: 24126688], suggesting incomplete penetrance. Homozygous or compound heterozygous occurrences of the variant likely lead to a more severe course of disease that may include lipomatosis and/or lipodystrophy. Functional studies using transfected fibroblasts have shown that the variant impairs MFN2-MFN2 protein interactions in mitochondria, making mitochondria prone to perinuclear aggregation [PMID: 26085578].
Clinical Genetics Laboratory, Skane University Hospital Lund	RCV000199654	SCV005199123	pathogenic	not provided	2022-05-27	criteria provided, single submitter	clinical testing
OMIM	RCV003231070	SCV000022527	pathogenic	Multiple symmetric lipomatosis	2008-05-06	no assertion criteria provided	literature only
GenomeConnect, ClinGen	RCV002508915	SCV002818389	not provided	Hereditary motor and sensory neuropathy with optic atrophy; Charcot-Marie-Tooth disease, type 2A		no assertion provided	phenotyping only	Variant classified as Likely pathogenic and reported on 03-29-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
OMIM	RCV000002369	SCV003929410	pathogenic	Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;	2008-05-06	no assertion criteria provided	literature only
Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino	RCV003319157	SCV004023245	likely pathogenic	Tip-toe gait	2022-06-14	no assertion criteria provided	clinical testing	Hereditary motor sensory neuropathy (HMSN), also known as Charcot-Marie-Tooth Disease (CMT), is the most commonly inherited peripheral polyneuropathy. It constitutes a group of inherited, progressive, motor and sensory peripheral nerve disorders with properties of demyelination, axonal degeneration, or both. It is classified by clinical characteristics, modes of inheritance, electrophysiologic features, metabolic defects, and specific gene markers. Our patients all walk on tiptoe, so they show similar symptoms. When we genetically test them with our toe walking panel, we find that around 90 per cent of them have a genetic variant that explains their toe walking. These can be assigned, for example, to the area of myopathies (such as variants of the COL6A3 gene), the area of hereditary neuropathies (such as variants of the KMT2C gene) or the area of metabolic diseases (such as variants of the PYGM gene). In a smaller group of patients with almost identical symptoms, no abnormality is found in the genes of our panel, but spastic paraplegia can be detected. In another small group of our toe walkers, no abnormalities can be detected in the genes analysed in our toe walking panel, nor do they suffer from spastic paraplegia, as is also the case with healthy children. In contrast to these, however, they show a tiptoe gait. These patients suffer from infantile cerebral palsy, in which toe walking can also be observed.
GenomeConnect - Invitae Patient Insights Network	RCV002285136	SCV004228536	not provided	Charcot-Marie-Tooth disease type 2A2; Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;		no assertion provided	phenotyping only	Variant interpreted as Pathogenic and reported on 03-02-2020 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.