ClinVar Genomic variation as it relates to human health

The RET c.1998G>T; p.Lys666Asn variant (rs146646971), is reported in the literature in individuals and families affected with medullary thyroid carcinoma and pheochromocytoma as a low penetetrance variant (Jaber 2018, Lebeault 2017, Muzza 2010, Xu 2016, Yehia 2018). This variant is reported as pathogenic or likely pathogenic by multiple laboratories in ClinVar (Variation ID: 24932), and is found in the non-Finnish European population with an allele frequency of 0.0054% (7/129,112 alleles) in the Genome Aggregation Database. Additionally, other amino acid substitutions at this codon (Glu, Arg, Met), as well as another variant at the same nucleotide (c.1998G>C; p.Lys666Asn), have been reported in individuals with RET-related disorders and are considered pathogenic or likely pathogenic (Ahmed 2005, Borrello 2011, Curras-Freixes 2015, Lebeault 2017, Mastroianno 2011, Wells 2015, Yamazaki 2014). The lysine at codon 666 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Functional analyses of the p.Lys666Asn variant protein show increased kinase and transforming activity (Muzza 2010). Based on available information, the p.Lys666Asn variant is considered to be likely pathogenic with reduced penetrance. References: Ahmed SA et al. Nine novel germline gene variants in the RET proto-oncogene identified in twelve unrelated cases. J Mol Diagn. 2005; 7(2):283-8. Borrello MG et al. Functional characterization of the MTC-associated germline RET-K666E mutation: evidence of oncogenic potential enhanced by the G691S polymorphism. Endocr Relat Cancer. 2011; 18(4):519-27. Curras-Freixes M et al. Recommendations for somatic and germline genetic testing of single pheochromocytoma and paraganglioma based on findings from a series of 329 patients. J Med Genet. 2015 Oct;52(10):647-56. Jaber T et al. A Homozygous RET K666N Genotype With an MEN2A Phenotype. J Clin Endocrinol Metab. 2018 Apr 1;103(4):1269-1272. Lebeault M et al. Nationwide French Study of RET Variants Detected from 2003 to 2013 Suggests a Possible Influence of Polymorphisms as Modifiers. Thyroid. 2017 Dec;27(12):1511-1522. Mastroianno S et al. Coexistence of multiple endocrine neoplasia type 1 and type 2 in a large Italian family. Endocrine. 2011; 40(3):481-5. Muzza M et al. Four novel RET germline variants in exons 8 and 11 display an oncogenic potential in vitro. Eur J Endocrinol. 2010; 162(4):771-7. Wells SA Jr et al. Revised American Thyroid Association guidelines for the management of medullary thyroid carcinoma. Thyroid. 2015; 25(6):567-610. Xu JY et al. Medullary Thyroid Carcinoma Associated with Germline RETK666N Mutation. Thyroid. 2016; 26(12):1744-1751. Yamazaki M et al. A newly identified missense mutation in RET codon 666 is associated with the development of medullary thyroid carcinoma. Endocr J. 2014; 61(11):1141-4. Yehia L et al. Unexpected cancer-predisposition gene variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients without underlying germline PTEN mutations. PLoS Genet. 2018 Apr 23;14(4):e1007352.

ACMG codes:PS3, PS4M, PM1, PP2, PP3, PP5

The variant has been reported as having low penetrance in multiple families affected with MTC, C-cell hyperplasia, or elevated calcitonin (PMIDs: 20103606 (2010), 27673361 (2016), and 28946813 (2017)). A family showing co-segregation included a homozygous MTC patient also affected with bilateral pheochromocytoma, which the authors described as a gene dosage effect (PMID: 29408964 (2018)). An individual presenting with pheochromocytoma and classic features of Cowden syndrome was also identified as a carrier of this variant (PMID: 29684080 (2018)). Additionally, functional studies have observed oncogenic effects resulting from this variant (PMID: 20103606 (2010)). Based on the available information, this variant is classified as pathogenic.

This c.1998G>G (p.Lys666Asn) variant in the RET gene has been reported in eight families with familial medullary thyroid carcinoma [PMID: 27673361]. This variant has also been reported in multiple clinical testing centers as disease-causing according to ClinVar while observed as extremely low in general population according to gnomad database. Functional studies showed this variant displays high kinase and transforming activities [PMID: 20103606]. Multiple in silico predictions suggest this lysine to asparagine is deleterious. Multiple disease-causing or risk associated variants have been reported to cause lysine at amino acid position 666 change to other amino acids in literatures[PMID: 15858153, 25319874, 25810047] and/or in ClinVar database. Based upon above evidences, c.1998G>G (p.Lys666Asn) variant in the RET gene is classified as likely pathogenic.

The p.Ly666Asn variant in RET has been reported in the heterozygous state in at least 10 individuals with MEN2-associated cancers, in the homozygous state in 1 individual with medullary thyroid cancer and bilateral pheochromocytoma and segregated with disease in 2 affected relatives from 2 families (Muzza 2010 PMID:20103606, Boichard 2012 PMID:22865907, Xu 2016 PMID:27673361, Jaber 2018 PMID:29408964, Lebault 2017 PMID:28946813). However, several other family members carried this variant but did not show evidence of disease, suggesting that this may be a low penetrance allele. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 24932) and has been identified in 0.005% (7/129112) European chromosomes by (gnomAD http://gnomad.broadinstitute.org). In vitro functional studies support an impact on protein function (Muzza 2010 PMID:20103606) and computational prediction tools and conservational analyses are consistent with pathogenicity. In addition, another likely pathogenic variant involving this codon (p.Lys666Glu) has been reported in individuals with MEN2-associated cancers and has been classified by the American Thyroid Association as imparting a moderate risk to developing aggressive medullary thyroid carcinoma (Wells 2015 PMID 25810047). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant multiple endocrine neoplasia type 2 (MEN2A), with reduced penetrance. ACMG criteria applied: PS4, PM2, PS3_Supporting, PM5_Supporting, PP1, PP3.

Variant summary: RET c.1998G>T (p.Lys666Asn) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.4e-05 in 251210 control chromosomes. c.1998G>T has been reported in the literature as a variant with low penetrance in multiple individuals affected with Familial Medullary Thyroid Carcinoma (example, Muzza_2010, Xu_2016, Jaber_2018) and as a homozygous variant in at-least one individual who presented with features of MTC and bilateral pheochromocytoma (PHEO) (example. Jaber_2018). These data indicate that the variant is very likely to be associated with disease. It has also been reported among variants with moderate risk in the revised American Thyroid Association guidelines for the management of Medullary Thyroid Carcinoma (Wells_2015). At least one publication reports experimental evidence evaluating an impact on protein function (Muzza_2010). The most pronounced variant effect results in a 13-fold increased rate of phosphorylation compared to WT-RET consistent with a gain of function mechanism of disease. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Published functional studies demonstrate increased tyrosine phosphorylation activity, kinase activity, and transforming potential compared to wild-type (Muzza et al., 2010); 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: 18631007, 21690267, 17934909, 21479187, 25637381, 26687385, 25319874, 21678021, 16954442, 17639053, 20103606, 29408964, 31447099, 28946813, 22865907, 29625052, 29684080, 27673361, 14633923, 34885201, 36451132, 30927507, 35668420)

This variant has been previously reported as a heterozygous change in multiple unrelated patients with medullary thyroid cancer (MTC), and as a homozygous change in one patient with MTC and bilateral pheochromocytoma (PMID: 27673361, 20103606, 29408964). The c.1998G>T (p.Lys666Asn) variant has been shown to segregate with disease in family members; however, it has also been observed in unaffected family members suggesting it may be a reduced penetrance allele (PMID: 27673361). Functional studies suggest this missense variant increases ERK and RET phosphorylation and cellular transformation (PMID: 20103606). Different amino acid changes at the same residue (p.K666E, p.K666R, and p.K666M) have reported in individuals with features of RET-related disorders (PMID: 15858153, 21690267, 24569963, 21678021, 25319874). The c.1998G>T (p.Lys666Asn) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.002% (7/282,120) and thus is presumed to be rare. It affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.1998G>T (p.Lys666Asn) variant is classified as Pathogenic.

The RET c.1998G>T (p.Lys666Asn) variant is reported in the literature in individuals and families affected with medullary thyroid carcinoma and pheochromocytoma as a low penetrance variant (Jaber T et al., PMID: 29408964; Lebeault M et al., PMID: 28946813; Muzza M et al., PMID: 20103606; Xu JY et al., PMID: 27673361). This variant has been reported in the ClinVar database as a germline pathogenic or likely pathogenic variant by 14 submitters. This variant is only observed on 7/282,120 alleles in the general population (gnomAD v.2.1.1), indicating it is not a common variant. Additionally, other amino acid substitutions at this codon (Arg, Asn, Glu, Met) have been reported in individuals with RET-related disorders and are considered pathogenic or likely pathogenic (Ahmed SA et al., PMID: 15858153., Borrello MG et al., PMID: 21690267; Lebeault M et al., PMID: 28946813, Mastroianno S et al., PMID: 21678021; Wells SA Jr et al., PMID: 25810047; Yamazaki M et al., PMID: 25319874). Computational predictors are uncertain as to the impact of this variant on RET function, but functional analyses of the p.Lys666Asn variant protein show increased kinase and transforming activity (Muzza M et al., PMID: 20103606). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic with low penetrance.

PP1_strong, PP4, PP5, PM1, PM2, PS3_supporting, PS4_moderate

This missense variant replaces lysine with asparagine at codon 666 of the RET protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). A functional study has reported that this variant protein resulted in elevated phosphorylation of the ERK protein in transiently-transfected at a level that is intermediate between the wild-type protein and the pathogenic control p.Cys634Arg (PMID: 20103606). The protein variant p.Lys666Asn, caused by c.1998G>T or c.1998G>C, has been reported in at least 14 unrelated heterozygous individuals affected with medullary thyroid cancer and/or pheochromocytoma (PMID: 20103606, 22865907, 26269449, 27673361, 28946813, 29408964) and a homozygous carrier affected with bilateral medullary thyroid cancer and pheochromocytoma (PMID: 29408964). This variant was also reported in an individual with Cowden syndrome clinical features (macrocephaly, lipoma, renal cancer, thyroid cancer, goiter and Hashimoto's thyroiditis) and pheochromocytoma (PMID: 29684080). This variant has been observed to segregate with medullary thyroid cancer, C-cell hyperplasia, elevated calcitonin and/or pheochromocytoma (PMID: 27673361, 29408964). This variant has been identified in 7/282120 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 666 of the RET protein (p.Lys666Asn). This variant is present in population databases (rs146646971, gnomAD 0.005%). This missense change has been observed in individuals with medullary thyroid cancer (PMID: 20103606, 26269449, 27673361; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 24932). 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 disruptive. Experimental studies have shown that this missense change affects RET function (PMID: 20103606). This variant disrupts the p.Lys666 amino acid residue in RET. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15858153, 21690267, 30927507). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 20103606]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 27673361, 29408964, 20103606].

The p.K666N pathogenic mutation (also known as c.1998G>T), located in coding exon 11 of the RET gene, results from a G to T substitution at nucleotide position 1998. The lysine at codon 666 is replaced by asparagine, an amino acid with similar properties. This specific alteration was identified in 8 unrelated index cases with medullary thyroid carcinoma (MTC) (Xu JY et al. Thyroid. 2016 Dec;36L1744-1751). Analysis of the families from these 8 cases showed several additional family members, who were carriers of the variant, also had either MTC or C-cell hyperplasia. Three carriers were shown to have normal pathology at ages 21, 30 and 30 years of age. Xu et al. conclude that this alteration is a low penetrance MTC allele, with no evidence for association with other MEN2A pathogenic features of pheochromocytoma and parathyroid abnormalities. This same alteration was reported in a case of sporadic medullary thyroid cancer in a 65 year old female (Muzza M et al. Eur J Endocrinol. 2010 Apr;162(4):771-7). Further analysis by Muzza et al. demonstrated increased oncogenic potential as compared to wild type, as well as significant structural impact that was predicted to alter the transmembrane &alpha;-helix, likely changing the secondary structure of the protein. In addition, several other alterations at this same position (p.K666E, p.K666R, and p.K666M) have been identified in sporadic cases of MTC (Yamazaki M et al. Endocr. J. 2014 Nov;61(11):1141-4; Borrello MG et al. Endocr. Relat. Cancer. 2011 Aug;18:519-27), or in large pedigrees demonstrating segregation with MTC or C-cell hyperplasia (Ahmed SA et al. J Mol Diagn. 2005 May;7(2):283-8; Mastroianno S et al. Endocrine. 2011 Dec;40:481-5). Of note, The American Thyroid Association has designated p.K666E as a mutation with moderate risk for MTC,10% incidence of pheochromocytomas and no incidence of hyperparathyroidism (Wells SA et al. Thyroid. 2015 Jun;25(6):567-610). As observed in the literature and Ambry internal data, p.K666N, is also primarily associated with MTC and not other features of MEN2A. Based on the supporting evidence, this alteration is classified as a pathogenic mutation with moderate risk for MEN2; however, the association of this alteration with Hirschsprung disease is unknown.

The c.1998G>T (p.Lys666Asn) variant in the RET gene is located on the exon 11 and is predicted to replace lysine with asparagine at codon 666 of the receptor tyrosine kinase RET. This variant has been reported in multiple families with familial medullary thyroid carcinoma (MTC) with incomplete penetrance (PMID: 20369307, 17895320, 25440022). Functional analysis of this variant showed increased kinase and transforming activities in transfected HEK293 cells (PMID: 20103606). An alternative nucleotide change resulting in the same amino acid change, c.1998G>C (p.Lys666Asn), has been classified as pathogenic/likely pathogenic (ClinVar ID: 230926). A distinct variant affecting the same codon, c.1996A>G (p.Lys666Glu), has also been reported to be pathogenic/likely pathogenic (ClinVar ID: 24931). This variant has been observed (7/282120) in the general population according to gnomAD. Based on these evidence, the c.1998G>T (p.Lys666Asn) variant in the RET gene is classified as likely pathogenic.

Variant classified as Pathogenic and reported on 07-08-2021 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

Variant interpreted as Pathogenic and reported on 07-30-2020 by 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.