ClinVar Genomic variation as it relates to human health

MITF c.952G>A (p.Glu318Lys variant, also referred to as Glu419Lys) in MITF has been associated with an increased risk of cutaneous melanoma. This variant has been observed in multiple ethnic backgrounds with highest frequencies in individuals of European ancestry (0.25%, Genome Aggregation Database (gnomAD); rs149617956) and is present in ClinVar (ID: 29792). Several large studies have reported an odds ratio of 1.7-5.5 for developing melanoma in heterozygous carriers (OR=2.19 [95% CI 1.41-3.45] Yokoyama 2011, OR=5.55 [95% CI 2.59-12.91] Bertolotto 2011, OR=1.7 [95% CI 1.1-2.6] Berwick 2011, OR=3.19 [95% CI 1.34-7.59] Castro-Vega 2016, OR=2.85 [95% CI 1.31-6.18] Ghiorzo 2013, OR=4.5 [95% CI 1.83-11.01] Potrony 2016). In vitro functional evidence suggests that the p.Glu318Lys variant reduces sumoylation of MITF, which in turn increases MITF transcriptional activity (Bertolotto 2011, Grill 2013, Yokoyama 2011). Therefore, this variant is not expected to cause highly penetrant Mendelian disease. In summary, this variant is an established risk factor for cutaneous melanoma.

PS3_Moderate, PS4, PP1_Moderate, PP3

In the published literature, this variant has been reported in multiple individuals with melanoma and/or renal cell carcinoma (PMIDs: 22012259 (2011), 22080950 (2011), 24638154 (2014), 26775776 (2016), 26800492 (2016), 27473757 (2016), 30414346 (2019), and 32054529 (2020)). Also, multiple case-control studies have shown that this variant is associated with an increased risk for melanoma and/or renal cell carcinoma (PMIDs: 22012259 (2011), 22080950 (2011), 23167872 (2013), 25803691 (2015), and 26650189 (2016)). In addition, functional studies have shown that this variant causes MITF protein overactivity (PMIDs: 22012259 (2011), 22080950 (2011), and 23787126 (2013)). Therefore, this variant is predicted to be pathogenic.

ACMG classification criteria: PS3 supporting, PS4 strong, PP1 moderated

The MITF c.1255G>A (p.Glu419Lys) missense change has a maximum population frequency of 0.25% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). This variant is known in the literature as NM_000248.4: c.952G>A (p.Glu318Lys). It has been reported in individuals with melanoma (PMID: 22012259, 22080950, 23167872, 23774529, 25803691, 26650189, 27473757), where the variant has been shown to segregate with disease in studies of families with multiple instances of melanoma (PMID: 22012259, 22080950, 23167872). In addition, case-control studies have indicated that individuals with this variant had a significantly increased risk of developing melanoma with an odds ratio of greater than 2 (PMID: 22080950). This variant has also been observed in individuals with a personal and/or family history of renal cell carcinoma (PMID: 22012259, 23167872, 26650189). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, but functional studies have shown decreased SUMOlation of MITF leading to elevated transcription of target genes as compared to the wild-type protein (PMID: 22012259, 22080950, 23787126). In summary, this variant meets criteria to be classified as pathogenic.

This variant is a recurrent alteration that has been reported as a heterozygous change in multiple individuals with cutaneous melanoma, renal cell carcinoma, or both cancers (PMID: 22012259, 22012259, 22080950, 27473757). A large case-controlled study observed that individuals with the p.Glu419Lys variant had a significantly increased risk of cutaneous melanoma (PMID: 22080950). Additionally, several studies showed the p.Glu419Lys variant had moderate co-segregation with melanoma, supporting the theory that this variant is a moderate penetrance melanoma risk factor (PMID: 22080950, 22012259, 23167872). Experimental studies have shown that the p.Glu419Lys variant leads to abnormal transcription of target genes and, in certain cell lines, increased colony forming potential (PMID: 22012259, 22080950, 23787126). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.1% (386/282776). In silico tools used to predict the effect of this variant on protein function yield discordant results. Based on the available evidence, the c.1255G>A (p.Glu419Lys) variant is classified as Pathogenic.

This missense variant replaces glutamic acid with lysine at codon 318 of the MITF protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that this variant decreases the SUMOylation of MITF, resulting in altered transcription of target genes and increased colony forming potential (PMID: 22012259, 22080950, 28376192). This variant has been reported in multiple individuals affected with cutaneous melanoma (PMID: 22012259, 22080950, 23774529, 24638154, 24660985, 25943250, 26103950, 26775776, 26800492, 27473757, 30414346), Ewing sarcoma (PMID: 28125078), pheochromocytomas/paragangliomas (PMID: 27680874), or renal cell carcinoma (PMID: 22012259). Multiple case-control studies have shown that this variant is associated with an increased risk of melanoma (PMID: 22012259, 22080950, 25803691, 26650189, 26775776). In addition, this variant is associated with an increased risk of renal cell carcinoma (PMID: 22012259). In a study of more than 30 families, this variant has been shown to have a moderate segregation with melanoma with LOD of 2.7 (PMID: 22080950). This variant is frequently observed in the general population and has been identified in 386/282776 chromosomes by the Genome Aggregation Database (gnomAD). In summary, this variant alters MITF protein function and is associated with an increased risk of melanoma and renal cell carcinoma. Based on the available evidence, this variant is classified as Likely Pathogenic.

The MITF c.952G>A; p.Glu318Lys variant (rs149617956) is reported in the literature in patients affected with renal cell carcinoma and sporadic and familial melanoma (Bertolotto 2011, Yokoyama 2011, Backman 2021, Bonet 2017). This variant is also reported in ClinVar (Variation ID: 29792) and is found in African, Latino, and European populations with an overall allele frequency of 0.14% (386/282776 alleles) in the Genome Aggregation Database. In vitro and in vivo functional analyses demonstrate the glutamic acid to lysine amino acid change results in defective SUMOylation of the MITF protein causing defective cellular senescence (Bertolotto 2011, Bonet 2017). Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.438). Based on available information, this variant is considered to be pathogenic. References: Bertolotto, C et al. A SUMOylation-defective MITF germline mutation predisposes to melanoma and renal carcinoma. Nature 480, 94-98 (2011). PMID: 22012259 Yokoyama S et al. A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma. Nature. 2011;480(7375):99-103. Published 2011 Nov 13. PMID: 22080950 Backman JD et al. Exome sequencing and analysis of 454,787 UK Biobank participants. Nature. 2021;599(7886):628-634. PMID: 34662886 Bonet C et al. Deciphering the Role of Oncogenic MITFE318K in Senescence Delay and Melanoma Progression. J Natl Cancer Inst. 2017;109(8). PMID: 28376192

ACMG Criteria: PS3, PS4, PP1, PP5; Variant was found in heterozygous state.

Published functional studies demonstrate a damaging effect: impaired sumoylation and differentially regulated expression of several MITF target genes (Bertolotto 2011, Yokoyama 2011, Grill 2013, Bonet 2017); Most case control studies suggest variant is associated with melanoma (OR=2.09-4.78), with an enrichment of the variant in patients with multiple primary melanomas and those with a family history of melanoma (Bertolotto 2011, Yokoyama 2011, Ghiorzo 2013, Gromowski 2014, Wadt 2015, Potrony 2016); Overrepresented among renal cell carcinoma cases (OR=5.19) and in individuals diagnosed with both melanoma and renal cell carcinoma (OR=14.46) (Bertolotto 2011); This variant is associated with the following publications: (PMID: 23787126, 27473757, 28125078, 28825054, 31034483, 22012259, 22080950, 28376192, 23167872, 24767713, 25803691, 26650189, 23774529, 24406078, 27153395, 27680874, 26800492, 27181379, 26775776, 26999813, 26999650, 27899189, 27720647, 28787086, 28152038, 24660985, 24290354, 23802662, 23046018, 22158021, 2440678, 24352080, 29485552, 29706638, 29506128, 30759220, 31201024, 30414346, 32054529, 31465090, 33240314)

This variant was identified in a 12 year old female with moderate intellectual disability, borderline microcephaly, ADHD, speech disorder, stereotypy, constipation, narrow face, upturned nose, and mildly bowed upper lip. It is present in the gnomAD non-Finnish European population at 0.25%. This variant is a well-established risk factor for melanoma and renal cell carcinoma (OR 2.95-8.37, depending on family history) (Bertolotto, 2011; Ghiorzo, 2013; Wadt, 2015; Potrony, 2016). This variant was also present in the proband's mother who had melanoma diagnosed in her early 30s.

PS3_supporting, PS4

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 318 of the MITF protein (p.Glu318Lys). This variant is present in population databases (rs149617956, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with autosomal dominant cutaneous melanoma (PMID: 22012259, 22080950, 23167872, 27473757). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 29792). 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 not expected to disrupt MITF protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects MITF function (PMID: 22012259, 22080950, 23787126). For these reasons, this variant has been classified as Pathogenic.

The MITF c.952G>A p.(Glu318Lys) variant, also referred to as c.1255G>A p.(Glu419Lys), is associated with increased risk for melanoma. Bertolotto et al. (2011) identified the p.(Glu318Lys) variant in a heterozygous state in 17 of 603 melanoma patients who were negative for CDKN2A and CDK4 variants. Carriers of this variant exhibited a significant increase in melanoma risk when compared to the control population, with an odds ratio of 4.78 [95% confidence interval: 2.05-11.75). The p.(Glu318Lys) variant was also found to co-segregate with melanoma in three melanoma-prone families. Yokoyama et al. (2011) identified 31 unrelated cases carrying the p.Glu318Lys variant who had at least one first- or second-degree relative diagnosed with melanoma. In 21 of 43 families, the variant was found in all affected individuals who were available for testing. Functional analysis showed that MITF encoded by the p.(Glu318Lys) variant allele had impaired sumoylation and differentially regulated several MITF targets. Berwick et al. (2014) assessed the p.(Glu318Lys) variant in 1194 cases and 2430 controls and found a positive association between the variant and the risk of melanoma, which was independent of the classical melanoma risk factors. Several additional studies have also reported a significantly increased melanoma risk in carriers of the variant (Ghiorzo et al. 2013; Potrony et al. 2015) or higher frequency of the variant in cases versus controls (Wadt et al. 2015). This variant has also been associated with an increased risk of renal cell carcinoma (Bertolotto et al. 2011; Ghiorzo et al. 2013; Potrony et al. 2016). The highest frequency of this allele in the Genome Aggregation Database is 0.002456 in the European (non-Finnish) population (version 2.1.1). Based on the available evidence, the c.952G>A p.(Glu318Lys) variant is classified as a pathogenic risk allele for melanoma.

The p.E318K pathogenic mutation (also known as c.952G>A), located in coding exon 9 of the MITF gene, results from a G to A substitution at nucleotide position 952. The glutamic acid at codon 318 is replaced by lysine, an amino acid with similar properties. Several case-control studies have identified an approximately 2-fold increased odds ratio for developing melanoma in carriers of MITF p.E318K compared to healthy controls (Ghiorzo P et al. Pigment Cell Melanoma Res. 2013 Mar;26:259-62; Bruno W et al. J. Am. Acad. Dermatol. 2016 Feb;74:325-32; Berwick M et al. Pigment Cell Melanoma Res. 2014 May;27:485-8; Potrony M et al. JAMA Dermatol. 2016 Apr;152:405-12; Mangas C et al. Br. J. Dermatol. 2016 Jul;175:1030-1037). This alteration segregates with melanoma in several families in a pattern that is consistent with a moderate penetrance allele, and has been identified in numerous unselected control groups across studies (Bertolotto C et al. Nature. 2011 Dec;480:94-8; Yokoyama S et al. Nature. 2011 Dec;480:99-103; Ghiorzo P et al. Pigment Cell Melanoma Res. 2013 Mar;26:259-62; Mangas C et al.). In addition, this variant has also been identified in numerous individuals in our internal cohort unaffected with RCC or melanoma (Ambry Internal Data). Though some studies have suggested an increase in risk of renal cell carcinoma, current evidence is insufficient to support a clear increase in risk of renal cancer in carriers of p.E318K over that of the general population (Bertolotto C et al; Guhan S et al. Sci Rep. 2020 Oct 13;10(1):17051). Functional analysis suggests that this variant prevents appropriate sumoylation, which leads to differential binding and activation of MITF target genes (Yokoyama S et al. Nature. 2011 Dec;480:99-103; Grill C et al. Hum. Mol. Genet. 2013 Nov;22:4357-67). In addition, this variant is shown to affect cellular senescence further promoting melanoma development (Bonet C et al. J. Natl. Cancer Inst. 2017 08;109). Based on the available evidence, this alteration is classified as a pathogenic mutation.

Variant summary: Variant summary: MITF c.952G>A (p.Glu318Lys) results in a conservative amino acid change located in the Myc-type, basic helix-loop-helix (bHLH) 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 262840 control chromosomes. This frequency is not higher than the estimated maximum expected for a pathogenic variant in MITF causing Melanoma and Renal Cell Carcinoma Risk (0.0014 vs 0.002), allowing no conclusion about variant significance. The variant c.952G>A has been reported in the literature in multiple individuals affected with melanoma and renal cell carcinoma (e.g. Bertolotto_2011, Yokoyama_2012, Ghiorzo_2012, Potjer_2018), where the variant was noted to segregate with the disease in some, but not all families, indicating that the E318K is a possible intermediate risk variant. In a large case-control study authors observed that individuals who carried the variant had significantly higher risk of developing melanoma (OR=2.19 CI: 1.41-3.45). Similarly, the carriers of this variant were reported to have a 5 fold increased risk of developing melanoma, renal cell carcinoma or both these cancers (OR = 5.55 (95% CI 2.59-12.91, Bertolotto_2011). The variant was also observed in individuals with personal and/or family history of breast cancer and other tumor phenotypes (Oliveira_2021), however a meta-analysis found minimal evidence for E318K's contribution to non-melanoma cancer risk (Guhan_2020). Experimental evidence suggests that this missense change causes decreased SUMOylation of MITF, resulting in an increased transcriptional activity with enhanced migration, invasion and colony formation in stable melanoma cells (Bertolotto_2011). In a series of in vitro studies performed by Grill et al, the variant showed normal DNA binding ability, but had promoter specific effects on transcription of its target genes (Grill_2013). Fourteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as pathogenic (n=9) / likely pathogenic (n=3) or as a risk factor (n=2). Based on the evidence outlined above, the variant appears to be a risk-factor for melanoma and/or renal cell carcinoma with supportive functional evidence. Therefore, it was classified as pathogenic.

MITF: PS3, PM1, PP1, PS4:Supporting

Variant identified in multiple registry participants. Variant interpreted as Likely pathogenic and reported on 01-03-2018 by Lab or GTR ID 505849 an interpreted as Pathogenic and reported on 09-18-2017 by Lab or GTR ID 61756. 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.

Variant interpreted as Pathogenic and reported on 10-29-2020 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.