NM_020975.6(RET):c.2488G>A (p.Gly830Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign (1 submission)
Last evaluated:: Apr 19, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002429338.2

Allele description [Variation Report for NM_020975.6(RET):c.2488G>A (p.Gly830Arg)]

NM_020975.6(RET):c.2488G>A (p.Gly830Arg)

Gene:

RET:ret proto-oncogene [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q11.21

Genomic location:

Preferred name:

NM_020975.6(RET):c.2488G>A (p.Gly830Arg)

HGVS:

NC_000010.11:g.43119626G>A
NG_007489.1:g.47558G>A
NM_000323.2:c.2488G>A
NM_001355216.2:c.1726G>A
NM_001406743.1:c.2488G>A
NM_001406744.1:c.2488G>A
NM_001406759.1:c.2488G>A
NM_001406760.1:c.2488G>A
NM_001406761.1:c.2359G>A
NM_001406762.1:c.2359G>A
NM_001406763.1:c.2353G>A
NM_001406764.1:c.2359G>A
NM_001406765.1:c.2353G>A
NM_001406766.1:c.2200G>A
NM_001406767.1:c.2200G>A
NM_001406768.1:c.2224G>A
NM_001406769.1:c.2092G>A
NM_001406770.1:c.2200G>A
NM_001406771.1:c.2050G>A
NM_001406772.1:c.2092G>A
NM_001406773.1:c.2050G>A
NM_001406774.1:c.1963G>A
NM_001406775.1:c.1762G>A
NM_001406776.1:c.1762G>A
NM_001406777.1:c.1762G>A
NM_001406778.1:c.1762G>A
NM_001406779.1:c.1591G>A
NM_001406780.1:c.1591G>A
NM_001406781.1:c.1591G>A
NM_001406782.1:c.1591G>A
NM_001406783.1:c.1462G>A
NM_001406784.1:c.1498G>A
NM_001406785.1:c.1471G>A
NM_001406786.1:c.1462G>A
NM_001406787.1:c.1456G>A
NM_001406788.1:c.1303G>A
NM_001406789.1:c.1303G>A
NM_001406790.1:c.1303G>A
NM_001406791.1:c.1183G>A
NM_001406792.1:c.1039G>A
NM_001406793.1:c.1039G>A
NM_001406794.1:c.1039G>A
NM_020629.2:c.2488G>A
NM_020630.7:c.2488G>A
NM_020975.6:c.2488G>AMANE SELECT
NP_000314.1:p.Gly830Arg
NP_001342145.1:p.Gly576Arg
NP_001342145.1:p.Gly576Arg
NP_001393672.1:p.Gly830Arg
NP_001393673.1:p.Gly830Arg
NP_001393688.1:p.Gly830Arg
NP_001393689.1:p.Gly830Arg
NP_001393690.1:p.Gly787Arg
NP_001393691.1:p.Gly787Arg
NP_001393692.1:p.Gly785Arg
NP_001393693.1:p.Gly787Arg
NP_001393694.1:p.Gly785Arg
NP_001393695.1:p.Gly734Arg
NP_001393696.1:p.Gly734Arg
NP_001393697.1:p.Gly742Arg
NP_001393698.1:p.Gly698Arg
NP_001393699.1:p.Gly734Arg
NP_001393700.1:p.Gly684Arg
NP_001393701.1:p.Gly698Arg
NP_001393702.1:p.Gly684Arg
NP_001393703.1:p.Gly655Arg
NP_001393704.1:p.Gly588Arg
NP_001393705.1:p.Gly588Arg
NP_001393706.1:p.Gly588Arg
NP_001393707.1:p.Gly588Arg
NP_001393708.1:p.Gly531Arg
NP_001393709.1:p.Gly531Arg
NP_001393710.1:p.Gly531Arg
NP_001393711.1:p.Gly531Arg
NP_001393712.1:p.Gly488Arg
NP_001393713.1:p.Gly500Arg
NP_001393714.1:p.Gly491Arg
NP_001393715.1:p.Gly488Arg
NP_001393716.1:p.Gly486Arg
NP_001393717.1:p.Gly435Arg
NP_001393718.1:p.Gly435Arg
NP_001393719.1:p.Gly435Arg
NP_001393720.1:p.Gly395Arg
NP_001393721.1:p.Gly347Arg
NP_001393722.1:p.Gly347Arg
NP_001393723.1:p.Gly347Arg
NP_065680.1:p.Gly830Arg
NP_065681.1:p.Gly830Arg
NP_065681.1:p.Gly830Arg
NP_065681.1:p.Gly830Arg
NP_066124.1:p.Gly830Arg
NP_066124.1:p.Gly830Arg
LRG_518t1:c.2488G>A
LRG_518t2:c.2488G>A
LRG_518:g.47558G>A
LRG_518p1:p.Gly830Arg
LRG_518p2:p.Gly830Arg
NC_000010.10:g.43615074G>A
NM_001355216.1:c.1726G>A
NM_020630.4:c.2488G>A
NM_020630.6:c.2488G>A
NM_020975.4:c.2488G>A

Protein change:

G347R

Links:

dbSNP: rs200127630

NCBI 1000 Genomes Browser:

rs200127630

Molecular consequence:

NM_000323.2:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001355216.2:c.1726G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406743.1:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406744.1:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406759.1:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406760.1:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406761.1:c.2359G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406762.1:c.2359G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406763.1:c.2353G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406764.1:c.2359G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406765.1:c.2353G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406766.1:c.2200G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406767.1:c.2200G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406768.1:c.2224G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406769.1:c.2092G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406770.1:c.2200G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406771.1:c.2050G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406772.1:c.2092G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406773.1:c.2050G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406774.1:c.1963G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406775.1:c.1762G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406776.1:c.1762G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406777.1:c.1762G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406778.1:c.1762G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406779.1:c.1591G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406780.1:c.1591G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406781.1:c.1591G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406782.1:c.1591G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406783.1:c.1462G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406784.1:c.1498G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406785.1:c.1471G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406786.1:c.1462G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406787.1:c.1456G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406788.1:c.1303G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406789.1:c.1303G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406790.1:c.1303G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406791.1:c.1183G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406792.1:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406793.1:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406794.1:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020629.2:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020630.7:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020975.6:c.2488G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002742233	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Apr 19, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22174939, 30217742 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002742233

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Apr 19, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

RET mutational spectrum in Hirschsprung disease: evaluation of 601 Chinese patients.

So MT, Leon TY, Cheng G, Tang CS, Miao XP, Cornes BK, Diem NN, Cui L, Ngan ES, Lui VC, Wu XZ, Wang B, Wang H, Yuan ZW, Huang LM, Li L, Xia H, Zhu D, Liu J, Nguyen TL, Chan IH, Chung PH, et al.

PLoS One. 2011;6(12):e28986. doi: 10.1371/journal.pone.0028986. Epub 2011 Dec 9.

PubMed [citation]

PMID:: 22174939
PMCID:: PMC3235168

Identification of Genes Associated With Hirschsprung Disease, Based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development.

Tang CS, Li P, Lai FP, Fu AX, Lau ST, So MT, Lui KN, Li Z, Zhuang X, Yu M, Liu X, Ngo ND, Miao X, Zhang X, Yi B, Tang S, Sun X, Zhang F, Liu H, Liu Q, Zhang R, Wang H, et al.

Gastroenterology. 2018 Dec;155(6):1908-1922.e5. doi: 10.1053/j.gastro.2018.09.012. Epub 2018 Sep 12.

PubMed [citation]

PMID:: 30217742

Details of each submission

From Ambry Genetics, SCV002742233.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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