rs149617956

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 8P and 2B. PP5_Very_StrongBP4BS1_Supporting

The NM_001354604.2(MITF):c.1273G>A(p.Glu425Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00278 in 1,614,114 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic,risk factor (★★).

Frequency

Genomes: 𝑓 0.0016 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0029 ( 9 hom. )

Consequence

MITF
NM_001354604.2 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic; risk factor criteria provided, multiple submitters, no conflicts P:25O:5

Conservation

PhyloP100: 8.01

Variant links:

Genes affected

MITF (HGNC:7105): (melanocyte inducing transcription factor) The protein encoded by this gene is a transcription factor that contains both basic helix-loop-helix and leucine zipper structural features. The encoded protein regulates melanocyte development and is responsible for pigment cell-specific transcription of the melanogenesis enzyme genes. Heterozygous mutations in the this gene cause auditory-pigmentary syndromes, such as Waardenburg syndrome type 2 and Tietz syndrome. [provided by RefSeq, Aug 2017]

MITF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PP5

Variant 3-69964940-G-A is Pathogenic according to our data. Variant chr3-69964940-G-A is described in ClinVar as [Likely_pathogenic, risk_factor]. Clinvar id is 29792.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-69964940-G-A is described in Lovd as [Pathogenic].

BP4

Computational evidence support a benign effect (MetaRNN=0.034677655). . Strength limited to SUPPORTING due to the PP5.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00158 (240/152232) while in subpopulation NFE AF= 0.00244 (166/68008). AF 95% confidence interval is 0.00214. There are 1 homozygotes in gnomad4. There are 96 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MITF	NM_001354604.2 link	c.1273G>A	p.Glu425Lys	missense_variant	Exon 10 of 10	ENST00000352241.9	NP_001341533.1
MITF	NM_000248.4 link	c.952G>A	p.Glu318Lys	missense_variant	Exon 9 of 9	ENST00000394351.9	NP_000239.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MITF	ENST00000352241.9 link	c.1273G>A	p.Glu425Lys	missense_variant	Exon 10 of 10	1	NM_001354604.2	ENSP00000295600.8		O75030-1
MITF	ENST00000394351.9 link	c.952G>A	p.Glu318Lys	missense_variant	Exon 9 of 9	1	NM_000248.4	ENSP00000377880.3		O75030-9

Frequencies

GnomAD3 genomes

AF:

0.00158

AC:

240

AN:

152114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00203

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00244

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00136

AC:

342

AN:

251388

Hom.:

AF XY:

0.00135

AC XY:

184

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.000491

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00249

Gnomad OTH exome

AF:

0.00147

GnomAD4 exome

AF:

0.00291

AC:

4251

AN:

1461882

Hom.:

Cov.:

AF XY:

0.00273

AC XY:

1983

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.000418

Gnomad4 AMR exome

AF:

0.000604

Gnomad4 ASJ exome

AF:

0.0000765

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000880

Gnomad4 NFE exome

AF:

0.00362

Gnomad4 OTH exome

AF:

0.00215

GnomAD4 genome

AF:

0.00158

AC:

240

AN:

152232

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00203

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00244

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00231

Hom.:

Bravo

AF:

0.00179

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00314

AC:

ExAC

AF:

0.00133

AC:

161

EpiCase

AF:

0.00278

EpiControl

AF:

0.00261

ClinVar

Significance: Pathogenic/Likely pathogenic; risk factor

Submissions summary: Pathogenic:25Other:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Melanoma, cutaneous malignant, susceptibility to, 8

Pathogenic:9Other:1

Nov 13, 2011

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Jan 03, 2022

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Jul 01, 2022

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Feb 17, 2023

Institute of Immunology and Genetics Kaiserslautern

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Mar 30, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 03, 2018

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

May 02, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Sep 26, 2022

HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

PS3_Moderate, PS4, PP1_Moderate, PP3 -

Jun 06, 2017

Geisinger Autism and Developmental Medicine Institute, Geisinger Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing;provider interpretation

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. -

not provided

Pathogenic:8Other:1

Mar 02, 2020

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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) -

Aug 06, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MITF c.952G>A; p.Glu318Lys variant (rs149617956, ClinVar variation ID: 29792) 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 found in the general population with an overall allele frequency of 0.14% (386/282776 alleles) in the Genome Aggregation Database (v2.1.1). 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 -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

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. -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 02, 2021

AiLife Diagnostics, AiLife Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 16, 2021

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Jan 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MITF: PP1:Strong, PS3:Moderate, PS4:Moderate -

Dec 11, 2023

Mayo Clinic Laboratories, Mayo Clinic

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3_supporting, PS4 -

Hereditary cancer-predisposing syndrome

Pathogenic:3

Mar 04, 2025

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. 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. -

Nov 22, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 supporting evidence, this variant is interpreted as a disease-causing mutation. -

Sep 17, 2019

Knight Diagnostic Laboratories, Oregon Health and Sciences University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Tietz syndrome;C1860339:Waardenburg syndrome type 2A;C3152204:Melanoma, cutaneous malignant, susceptibility to, 8

Pathogenic:1

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 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). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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. -

MITF-related disorder

Pathogenic:1

Nov 24, 2023

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant results in a c.1273G>A (p.Glu425Lys) and a c.952G>A (p.Glu318Lys) change in alternate transcripts (NM_001354604.2, NM_000248.4). The c.1255G>A (p.Glu419Lys) variant affects a highly conserved amino acid; however, in silico tools used to predict the effect of this variant on protein function yield discordant results. This variant is a recurrent alteration that has been reported as a heterozygous change in multiple individuals with cutaneous melanoma and/or renal cell carcinoma (PMID: 22012259, 22080950, 27473757). A large case-controlled study involving approximately 4,000 participants observed that individuals with the c.1255G>A (p.Glu419Lys) variant had a significantly increased risk of cutaneous melanoma (OR=2.19 CI: 1.41-3.45) (PMID: 22080950). Additionally, several studies of families harboring this variant showed the variant had moderate co-segregation with melanoma (LOD = 2.7), providing evidence to support c.1255G>A (p.Glu419Lys) as an intermediate penetrance melanoma risk variant (PMID: 22080950, 22012259, 23167872). Experimental studies have shown that this missense change decreases the SUMOylation of MITF, leading to elevated transcription of target genes and increased colony forming potential in certain cell lines (PMID: 22012259, 22080950, 23787126). This variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.1% (386/282776) and is absent in the homozygous state. Based on the available evidence, the c.1255G>A (p.Glu419Lys) variant is classified as Pathogenic. -

Tietz syndrome

Pathogenic:1

May 04, 2022

Mendelics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Tietz syndrome;C1860339:Waardenburg syndrome type 2A;C3152204:Melanoma, cutaneous malignant, susceptibility to, 8;C4310625:Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness

Pathogenic:1

Jan 09, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial melanoma

Pathogenic:1

Sep 20, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Other:1

Nov 25, 2019

PreventionGenetics, part of Exact Sciences

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Waardenburg syndrome type 2A;C3152204:Melanoma, cutaneous malignant, susceptibility to, 8

Other:1

GenomeConnect - Invitae Patient Insights Network

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

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. -

Melanoma

Other:1

Mar 04, 2020

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: risk factor

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.61

BayesDel_addAF

Uncertain

0.013

BayesDel_noAF

Pathogenic

0.25

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.85

.;D;.;.;.;.;.;.;.

Eigen

Pathogenic

0.94

Eigen_PC

Pathogenic

0.93

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Pathogenic

1.0

.;D;D;D;D;D;D;D;D

M_CAP

Benign

0.065

MetaRNN

Benign

0.035

T;T;T;T;T;T;T;T;T

MetaSVM

Uncertain

0.018

MutationAssessor

Pathogenic

3.0

.;M;.;.;.;.;.;.;.

PrimateAI

Uncertain

0.68

PROVEAN

Benign

-1.9

N;N;.;N;N;N;N;N;N

REVEL

Uncertain

0.44

Sift

Benign

0.039

D;D;.;D;T;D;D;D;D

Sift4G

Benign

0.081

T;T;.;T;T;T;T;T;T

Polyphen

0.98

D;.;D;.;D;D;D;D;.

Vest4

0.81

MVP

0.76

MPC

1.0

ClinPred

0.049

GERP RS

6.2

Varity_R

0.44

gMVP

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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