10-43114598-G-C

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS1PM5PP3_StrongPP5_Very_Strong

The NM_020975.6(RET):c.1998G>C(p.Lys666Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,612,836 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 (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in Lovd. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K666M) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

RET
NM_020975.6 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13O:1

Conservation

PhyloP100: 1.53

Variant links:

Genes affected

RET (HGNC:9967): (ret proto-oncogene) This gene encodes a transmembrane receptor and member of the tyrosine protein kinase family of proteins. Binding of ligands such as GDNF (glial cell-line derived neurotrophic factor) and other related proteins to the encoded receptor stimulates receptor dimerization and activation of downstream signaling pathways that play a role in cell differentiation, growth, migration and survival. The encoded receptor is important in development of the nervous system, and the development of organs and tissues derived from the neural crest. This proto-oncogene can undergo oncogenic activation through both cytogenetic rearrangement and activating point mutations. Mutations in this gene are associated with Hirschsprung disease and central hypoventilation syndrome and have been identified in patients with renal agenesis. [provided by RefSeq, Sep 2017]

RET links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PS1

Transcript NM_020975.6 (RET) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in Lovd

PM5

Other missense variant is known to change same aminoacid residue: Variant chr10-43114597-A-T is described in Lovd as [Pathogenic].

PP3

MetaRNN computational evidence supports a deleterious effect, 0.946

PP5

Variant 10-43114598-G-C is Pathogenic according to our data. Variant chr10-43114598-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 230926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RET	NM_020975.6 link	c.1998G>C	p.Lys666Asn	missense_variant	Exon 11 of 20	ENST00000355710.8	NP_066124.1	P07949-1A0A024R7T2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RET	ENST00000355710.8 link	c.1998G>C	p.Lys666Asn	missense_variant	Exon 11 of 20	5	NM_020975.6	ENSP00000347942.3		P07949-1

Frequencies

GnomAD3 genomes

AF:

0.00000658

AC:

AN:

152056

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000655

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000548

AC:

AN:

1460780

Hom.:

Cov.:

AF XY:

0.00000826

AC XY:

AN XY:

726704

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000540

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00000658

AC:

AN:

152056

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000655

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000151

ExAC

AF:

0.00000824

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Multiple endocrine neoplasia, type 2

Pathogenic:4

Jun 20, 2019

Hadassah Hebrew University Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with medullary thyroid carcinoma, C-cell dysplasia, and elevated calcitonin levels and pheochromocytoma (PMID: 20103606, 26269449, 26687385, 27673361). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 230926). 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). 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. -

Jul 10, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces lysine with asparagine at codon 666 of the RET protein. Computational predictions are inconclusive regarding the impact of this variant on protein structure and function and pre-mRNA splicing. A functional study has reported that this variant protein resulted in elevated kinase and cell transformation activities that were intermediate between the wild-type protein and the pathogenic control p.Cys634Arg (PMID: 20103606). The protein variant p.Lys666Asn, caused by c.1998G>C or c.1998G>T, has been reported in at least 13 unrelated individuals affected with medullary thyroid cancer (PMID: 20103606, 22865907, 27673361, 28946813, 29408964) and two individuals each affected with pheochromocytoma or C-cell hyperplasia (PMID: 26269449, 27673361, 29408964). This variant also has been reported in a homozygous carrier affected with medullary thyroid cancer and bilateral pheochromocytoma (PMID: 29408964) and an individual affected with clinical features of Cowden syndrome, including thyroid cancer, and also pheochromocytoma (PMID: 29684080). This variant is also has been described as incompletely penetrant, having been observed in over a dozen unaffected heterozygous carriers (PMID: 27673361, 29408964). Two different protein variants at codon 666, p.Lys666Glu and p.Lys666delinsAsnSer, have been reported in individuals affected with medullary thyroid cancer and are suspected to have more severe disease characteristics due a co-occurring polymorphism p.Gly691Ser (PMID: 15844786, 21690267), raising the possibility that substitutions at this codon may have variable penetrance or expressivity due to effects of genetic modifier. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Aug 17, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 the variant protein, p.Lys666Asn, 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 more than 10 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). The protein change 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), and it was 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. -

Multiple endocrine neoplasia type 2A

Pathogenic:2

Sep 15, 2022

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS1 strong, PS4 moderated, PM1 moderated, PM2 moderated -

Jan 05, 2024

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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]. -

MEN2 phenotype: Unclassified

Pathogenic:1

Aug 05, 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: RET c.1998G>C (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 was absent in 250810 control chromosomes (gnomAD). c.1998G>C has been reported in the literature in multiple individuals affected with Multiple Endocrine Neoplasia Type 2 (e.g. Boichard_2012, Curras_2015, Jaber_2018, Rosen_2022). These data indicate that the variant is very likely to be associated with disease. A different variant resulting in the same amino acid consequence has been classified as pathogenic by our lab (c.1998G>T), supporting the pathogenicity of this variant. The following publications have been ascertained in the context of this evaluation (PMID: 26269449, 29408964, 22865907, 35304457). ClinVar contains an entry for this variant (Variation ID: 230926). Based on the evidence outlined above, the variant was classified as pathogenic. -

Multiple endocrine neoplasia type 2A;C0025269:Multiple endocrine neoplasia type 2B;C0031511:Pheochromocytoma;C1833921:Familial medullary thyroid carcinoma;C3888239:Hirschsprung disease, susceptibility to, 1

Pathogenic:1

Jan 24, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hirschsprung disease, susceptibility to, 1

Pathogenic:1

Mar 12, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial medullary thyroid carcinoma

Pathogenic:1

Sep 23, 2020

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The inherited c.1998G>C,p.Lys666Asn missense variant identified in RET has been reported to segregate with medullary thyroid carcinoma, C-cell dysplasia, and elevated calcitonin levels in several families (PMID:27673361, 20103606). This variant has also been reported in individuals with pheochromocytoma (PMID:26269449) and breast cancer (PMID:26687385). This variant is present in population database (gnomAD v2.1) with a frequency of 0.002%. Experimental studies have shown that this missense variant results in increased RET phosphorylation activity and increased transformation potential in cell culture (PMID:20103606). Rare missense variants at the same codon (p.Lys666Glu, p.Lys666Met, p.Lys666Arg) have been reported in the individuals with medullary thyroid carcinoma and multiple endocrine neoplasia type II and suggests that the lysine residue is critical for RET protein function (PMID:15858153, 21690267, 21678021, 20516206, 25319874). Based on the available evidence, the inherited missense variant c.1998G>C,p.Lys666Asn in the RET gene is classified as Pathogenic. -

Hereditary cancer-predisposing syndrome

Pathogenic:1

Mar 22, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.K666N mutation (also known as c.1998G>C) is located in coding exon 11 of the RET gene. This alteration results from a G to C 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 one patient from a screen of 329 patients with sporadic paraganglioma or pheochromocytoma (Currás-Freixes M et al. J. Med. Genet., 2015 Oct;52:647-56). A similar alteration causing the same amino acid change (c.1998G>T p.K666N) was identified in eight unrelated index cases with medullary thyroid carcinoma (MTC) (Xu JY et al. Thyroid, 2016 Oct, epub). Analysis of the families from these 8 cases showed several additional family members who were carriers of the variant that 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 low penetrance MTC allele, with no evidence for association with other MEN2A pathogenic features of pheochromocytoma and parathyroid abnormalities. This same c.1998G>T p.K666N 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 α-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 primarily associated with MTC and not other features of MEN2A. Based on the available evidence, this alteration is classified as a pathogenic mutation with moderate risk. -

Multiple endocrine neoplasia type 2A;C0025269:Multiple endocrine neoplasia type 2B;C0031511:Pheochromocytoma;C1833921:Familial medullary thyroid carcinoma

Pathogenic:1

Nov 10, 2022

Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

RET-related disorder

Pathogenic:1

Mar 14, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The RET c.1998G>C variant is predicted to result in the amino acid substitution p.Lys666Asn. This variant has been reported in the heterozygous state in several individuals with a personal and family history of medullary thyroid cancer (MTC), and an in vitro assay showed it displayed high kinase and transforming activity (Muzza et al. 2010. PubMed ID: 20103606; Xu et al. 2016. PubMed ID: 27673361). This variant was also reported in a cohort of individuals with phaeochromocytoma (Curras-Freixes et al. 2015. PubMed ID: 26269449, supplementary data) and in cohorts of individuals with breast cancer (Bernstein-Molho et al. 2019. PubMed ID: 30980208; Yablonski-Peretz et al. 2016. PubMed ID: 26687385). Lastly, this variant was reported in the homozygous state in an individual with medullary thyroid cancer and bilateral pheochromocytoma; the patient's son, who carried this variant in the heterozygous state, also had MTC (Jaber et al. 2018. PubMed ID: 29408964). However, not all carriers of this variant were affected at the time of testing, suggesting potential incomplete penetrance or variable age at onset. Other amino acid substitutions at this position have been reported in individuals with MTC or pheochromocytoma, suggesting that this amino acid residue may be critical for function (Human Gene Mutation Database; https://www.hgmd.cf.ac.uk/). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/230926/?new_evidence=true). This variant is interpreted as likely pathogenic. -

Multiple endocrine neoplasia type 2A;C0025269:Multiple endocrine neoplasia type 2B;C1833921:Familial medullary thyroid carcinoma

Other:1

GenomeConnect - Brain Gene Registry

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Pathogenic and reported on 11-17-2020 by Lab or GTR ID New York Genome Center. 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 John Constantino MD PhD 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/. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.53

BayesDel_addAF

Uncertain

0.049

BayesDel_noAF

Benign

-0.17

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.72

D;.

Eigen

Benign

0.058

Eigen_PC

Benign

-0.020

FATHMM_MKL

Uncertain

0.86

LIST_S2

Uncertain

0.91

D;D

M_CAP

Uncertain

0.12

MetaRNN

Pathogenic

0.95

D;D

MetaSVM

Uncertain

-0.26

MutationAssessor

Benign

1.5

L;L

PrimateAI

Uncertain

0.55

PROVEAN

Uncertain

-2.6

D;D

REVEL

Uncertain

0.57

Sift

Uncertain

0.019

D;D

Sift4G

Uncertain

0.020

D;D

Polyphen

1.0

D;D

Vest4

0.68

MutPred

0.83

Loss of methylation at K666 (P = 0.0018);Loss of methylation at K666 (P = 0.0018);

MVP

0.86

MPC

0.78

ClinPred

0.96

GERP RS

1.6

Varity_R

0.38

gMVP

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.20

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.20

Position offset: 17

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

Other links and lift over