10-43114501-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2PM5PP3_StrongPP5_Very_Strong

The NM_020975.6(RET):​c.1901G>A​(p.Cys634Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,455,706 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C634F) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

RET
NM_020975.6 missense

Scores

11
6
2

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:24

Conservation

PhyloP100: 9.74
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr10-43114501-G-T is described in Lovd as [Pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.991
PP5
Variant 10-43114501-G-A is Pathogenic according to our data. Variant chr10-43114501-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 13909.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-43114501-G-A is described in Lovd as [Pathogenic]. Variant chr10-43114501-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RETNM_020975.6 linkc.1901G>A p.Cys634Tyr 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
RETENST00000355710.8 linkc.1901G>A p.Cys634Tyr missense_variant Exon 11 of 20 5 NM_020975.6 ENSP00000347942.3 P07949-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000404
AC:
1
AN:
247574
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134198
show subpopulations
Gnomad AFR exome
AF:
0.0000616
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1455706
Hom.:
0
Cov.:
32
AF XY:
0.00000276
AC XY:
2
AN XY:
724436
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:24
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Multiple endocrine neoplasia type 2A Pathogenic:8
May 09, 2002
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Nov 01, 2016
Center for Human Genetics, Inc, Center for Human Genetics, Inc
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Aug 30, 2017
Counsyl
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 21, 2023
Laboratory of Molecular and Cytogenetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS)
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 20, 2023
Neuberg Centre For Genomic Medicine, NCGM
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The observed missense c.1901G>A (p.Cys634Tyr) variant in RET gene has been reported in multiple individuals affected with RET-related disorders (Chiefari et al., 1998; Sánchez et al., 1999; Jackson et al., 2005; Valente et al., 2013; Valdés et al., 2015). It has also been observed to segregate with disease in related individuals (Valente et al., 2013). Amino acid position 634 is a well described mutation hot spot associated with Multiple endocrine neoplasia type 2A (MEN2A). Functional characterization of the p.Cys634Tyr variant and other missense variants at the same amino acid position (p.Cys634Arg, p.Cys634Trp) indicated increased auto-phosphorylation and activation of downstream targets, resulting in enhanced malignant transformation of cells (Cosci et al., 2011, Santoro et al., 1995). This variant is present with allele frequency of 0.0004% in gnomAD Exomes. This variant has been reported to the ClinVar database as Likely Pathogenic/ Pathogenic (multiple submissions). Multiple lines of computational evidence (Polyphen - Probably Damaging, SIFT - Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. The reference amino acid of p.Cys634Tyr in RET is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Cys at position 634 is changed to a Tyr changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -

Sep 01, 2021
MGZ Medical Genetics Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 18, 2019
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.1901G>A (p.Cys634Tyr) results in a non-conservative amino acid change located in the extracellular domain 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 4e-06 in 247574 control chromosomes. c.1901G>A has been well reported in the literature in multiple individuals affected with Multiple Endocrine Neoplasia Type 2A (example Chiefari_1998, Frank-Raue_2006). These data indicate that the variant is strongly associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function demonstrating a gain of function mechanism due to activation of the RET proto-oncogene (example Santoro_1995). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Apr 18, 2023
Myriad Genetics, Inc.
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID: 9230192, 21834681]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 26732158, 17188172, 34439168, 20801952, 33827484, 25810047]. -

not provided Pathogenic:7
Mar 24, 2023
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Published functional studies demonstrate a damaging effect: high transforming ability, constitutive kinase activation (Santoro 1995, Ito 1997); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as p.(Cys380Tyr); This variant is associated with the following publications: (PMID: 12711285, 8797874, 9146685, 23723040, 19062722, 27558615, 25515555, 26254625, 29133048, 29656518, 23330657, 7835899, 21765987, 7824936, 8099202, 15858153, 8626834, 21054478, 16314641, 17895320, 24716929, 12000816, 7874109, 20080836, 26732158, 28099363, 26758973, 26572832, 26876062, 27539324, 23868299, 11987030, 30139385, 29197744, 7881414, 9230192, 28469506, 30113649, 21655256, 18063059, 12686527, 9950371, 7860065, 16099853, 11524247, 19240193, 7914213, 7491519, 12604374, 9820617, 9699127, 31062739, 30122763, 16158949, 20516206, 29625052, 31510104, 32989896, 8909322, 18096130, 9497883, 8984233, 35627249, 28152038, 30763276, 9706252, 25545346, 33340421, 33219105, 35418818, 14633923) -

Dec 01, 2023
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The RET c.1901G>A;p.Cys634Tyr variant (rs75996173) is reported in the literature in multiple individuals and families with multiple endocrine neoplasia type 2 (MEN2) and familial medullary thyroid carcinoma (American Thyroid Association Guidelines Task Force 2009, Punales 2003, Wells 2015). This variant is found on a single chromosome in the Genome Aggregation Database (1/247574 alleles), indicating it is not a common polymorphism. The cysteine at codon 634 is highly conserved, and other amino acid substitutions at this codon (Arg, Gly, Phe, Ser, Trp) are considered causative for MEN2A (Wells 2015). Functional characterization of the p.Cys364Tyr variant and other missense variants at the same codon (p.Cys634Arg, p.Cys634Trp) indicates increased auto-phosphorylation and activation of downstream targets (Santoro 1995), resulting in enhanced malignant transformation of cells (Cosci 2011, Santoro 1995). Based on available information, the p.Cys634Tyr variant is considered to be pathogenic. References: American Thyroid Association Guidelines Task Force et al. Medullary thyroid cancer: management guidelines of the American Thyroid Association. Thyroid. 2009 Jun;19(6):565-612. PMID: 19469690. Cosci B et al. In silico and in vitro analysis of rare germline allelic variants of RET oncogene associated with medullary thyroid cancer. Endocr Relat Cancer. 2011 Sep 20;18(5):603-12. PMID: 21810974. Punales MK et al. RET codon 634 mutations in multiple endocrine neoplasia type 2: variable clinical features and clinical outcome. J Clin Endocrinol Metab. 2003 Jun;88(6):2644-9. PMID: 12788868. Santoro M et al. Activation of RET as a dominant transforming gene by germline mutations of MEN2A and MEN2B. Science. 1995 Jan 20;267(5196):381-3. PMID: 7824936. Wells S et al. Revised American Thyroid Association Guidelines for the Management of Medullary Thyroid Carcinoma. Thyroid. 2015; 25(6):567-610. PMID: 25810047. -

Apr 02, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 27, 2024
Athena Diagnostics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The frequency of this variant in the general population is consistent with pathogenicity. (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)) This variant has been identified in multiple unrelated individuals with MEN2A. The American Thyroid Association has placed this variant into the ATA-H category, formerly known as level C, for having a high risk of developing aggressive medullary thyroid carcinoma (MTC; see PMID: 25810047). At least one other missense variant at this codon is considered to be pathogenic or likely pathogenic, suggesting this variant may also cause disease. This variant segregates with disease in multiple families. Assessment of experimental evidence suggests this variant results in abnormal protein function. (PMID: 7824936, 9230192) -

May 18, 2023
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The RET c.1901G>A (p.Cys634Tyr) variant has been reported in the published literature in multiple individuals with MEN2A and/or FMTC (PMID: 7835899 (1994), 9950371 (1999), 12000816 (2002), 21765987 (2011), 25810047 (2015), 26732158 (2016), 28099363 (2017), 33167350 (2020)). A functional study found the variant has a damaging effect on RET function (PMID: 7824936 (2015)). The frequency of this variant in the general population, 0.000004 (1/247574 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. -

-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Multiple endocrine neoplasia type 2B Pathogenic:2
-
Suma Genomics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 07, 2023
KCCC/NGS Laboratory, Kuwait Cancer Control Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The family RET mutation (C634Y) was detected in this blood specimen. This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 634 of the RET protein (p.Cys634Tyr). This variant is present in population databases (rs75996173, gnomAD 0.007%). This missense change has been observed in individual(s) with multiple endocrine neoplasia type 2A and medullary thyroid cancer and pheochromocytoma (PMID: 2008030, 8099202, 12000816, 23723040). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13909) with 22 submissions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects RET function (PMID: 7824936). This variant disrupts the p.Cys634 amino acid residue in RET. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8099202, 12000816, 21765987). Therefore, this variant has been classified as Pathogenic. -

Pheochromocytoma Pathogenic:2
Oct 06, 2021
Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

May 09, 2002
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Hirschsprung disease, susceptibility to, 1 Pathogenic:2
Mar 26, 2024
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Dec 29, 2023
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Multiple endocrine neoplasia, type 2 Pathogenic:1
Nov 06, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 634 of the RET protein (p.Cys634Tyr). This variant is present in population databases (rs75996173, gnomAD 0.007%). This missense change has been observed in individual(s) with multiple endocrine neoplasia type 2A and medullary thyroid cancer and pheochromocytoma (PMID: 2008030, 8099202, 12000816, 23723040). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13909). 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 tolerated. Experimental studies have shown that this missense change affects RET function (PMID: 7824936). This variant disrupts the p.Cys634 amino acid residue in RET. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8099202, 12000816, 21765987). 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. -

Hereditary cancer-predisposing syndrome Pathogenic:1
Jun 06, 2022
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.C634Y pathogenic mutation (also known as c.1901G>A) is located in coding exon 11 of the RET gene. This alteration results from a G to A substitution at nucleotide position 1901. The cysteine at codon 634 is replaced by tyrosine, an amino acid with highly dissimilar properties. The p.C634Y mutation has been reported in several unrelated families diagnosed with MEN2A and/or familial medullary thyroid carcinoma (FMTC) (Mulligan et al. Nature. 1993;363:458-460; Marsh DJ et al. Genomics. 1994;23(2):477-479; Hedayati et al. J Thyroid Res. 2011;2011:264248; Sriphrapradang C et al. Clin Med Insights Endocrinol Diabetes. 2017 Apr;10:1179551417705122). Amino acid position 634 is a well described mutation hot spot associated with MEN2A/FMTC. Studies evaluating genotype-phenotype correlation suggest higher penetrance for pheochromocytoma in MEN2 patients with mutations at amino acid position 634 (Neumann HP et al. N. Engl. J. Med. 2002;346:1459-66, Quayle FJ et al. Surgery 2007;142:800-5; Yip L et al. Arch Surg 2003;138:409-16). Revised American Thyroid Association Guidelines categorize the p.C634Y alteration as high risk (ATA-H) and recommend surveillance and prophylactic surgery in early childhood (Wells SA et al. Thyroid 2015 Jun;25(6):567-610). Of note, this alteration has been referred to as p.C380Y (c.1832G>A) and p.C634Y (c.2096G>A) in the published literature. Based on the available evidence, p.C634Y is classified as a pathogenic mutation. -

RET-related disorder Pathogenic:1
Jun 24, 2024
PreventionGenetics, part of Exact Sciences
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The RET c.1901G>A variant is predicted to result in the amino acid substitution p.Cys634Tyr. This variant has been reported in multiple individuals with MEN2A, medullary thyroid cancer, and pheochromocytoma (Mulligan et al. 1993. PubMed ID: 8099202; Sanchez et al. 1999. PubMed ID: 9950371; Toledo et al. 2010. PubMed ID: 20080836). Functional studies have shown this variant and other amino acid changes at this position result in increased auto-phosphorylation and activation of downstream targets which enhances malignant transformation of cells (Santoro M et al. 1995. PubMed ID: 7824936; Cosci B et al. 2011. PubMed ID: 21810974). This variant is present in one individual in the gnomAD database. This variant is classified as pathogenic in ClinVar with multiple submitters in agreement (https://www.ncbi.nlm.nih.gov/clinvar/variation/13909/). We interpret this variant to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.73
BayesDel_addAF
Pathogenic
0.43
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.90
D;D;.
Eigen
Pathogenic
0.70
Eigen_PC
Uncertain
0.62
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.71
T;T;T
M_CAP
Pathogenic
0.82
D
MetaRNN
Pathogenic
0.99
D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.7
M;.;M
PrimateAI
Uncertain
0.79
T
PROVEAN
Pathogenic
-7.0
D;D;D
REVEL
Pathogenic
0.92
Sift
Uncertain
0.0010
D;D;D
Sift4G
Pathogenic
0.0010
D;D;D
Polyphen
1.0
D;.;D
Vest4
0.99
MutPred
0.95
Gain of catalytic residue at C634 (P = 0.0096);.;Gain of catalytic residue at C634 (P = 0.0096);
MVP
0.97
MPC
0.45
ClinPred
0.98
D
GERP RS
3.6
Varity_R
0.86
gMVP
0.96

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.

Other links and lift over

dbSNP: rs75996173; hg19: chr10-43609949; COSMIC: COSV60688821; API