NM_020975.6(RET):c.539G>A (p.Arg180Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 11, 2023
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:: RCV003736605.1

Allele description [Variation Report for NM_020975.6(RET):c.539G>A (p.Arg180Gln)]

NM_020975.6(RET):c.539G>A (p.Arg180Gln)

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.539G>A (p.Arg180Gln)

HGVS:

NC_000010.11:g.43102543G>A
NG_007489.1:g.30475G>A
NM_000323.2:c.539G>A
NM_001406743.1:c.539G>A
NM_001406744.1:c.539G>A
NM_001406759.1:c.539G>A
NM_001406760.1:c.539G>A
NM_001406761.1:c.410G>A
NM_001406762.1:c.410G>A
NM_001406763.1:c.539G>A
NM_001406764.1:c.410G>A
NM_001406765.1:c.539G>A
NM_001406768.1:c.410G>A
NM_001406769.1:c.539G>A
NM_001406771.1:c.539G>A
NM_001406772.1:c.539G>A
NM_001406773.1:c.539G>A
NM_001406774.1:c.410G>A
NM_001406779.1:c.539G>A
NM_001406780.1:c.539G>A
NM_001406781.1:c.539G>A
NM_001406782.1:c.539G>A
NM_001406783.1:c.410G>A
NM_001406785.1:c.539G>A
NM_001406786.1:c.410G>A
NM_001406787.1:c.539G>A
NM_020629.2:c.539G>A
NM_020630.7:c.539G>A
NM_020975.6:c.539G>AMANE SELECT
NP_000314.1:p.Arg180Gln
NP_001393672.1:p.Arg180Gln
NP_001393673.1:p.Arg180Gln
NP_001393688.1:p.Arg180Gln
NP_001393689.1:p.Arg180Gln
NP_001393690.1:p.Arg137Gln
NP_001393691.1:p.Arg137Gln
NP_001393692.1:p.Arg180Gln
NP_001393693.1:p.Arg137Gln
NP_001393694.1:p.Arg180Gln
NP_001393697.1:p.Arg137Gln
NP_001393698.1:p.Arg180Gln
NP_001393700.1:p.Arg180Gln
NP_001393701.1:p.Arg180Gln
NP_001393702.1:p.Arg180Gln
NP_001393703.1:p.Arg137Gln
NP_001393708.1:p.Arg180Gln
NP_001393709.1:p.Arg180Gln
NP_001393710.1:p.Arg180Gln
NP_001393711.1:p.Arg180Gln
NP_001393712.1:p.Arg137Gln
NP_001393714.1:p.Arg180Gln
NP_001393715.1:p.Arg137Gln
NP_001393716.1:p.Arg180Gln
NP_065680.1:p.Arg180Gln
NP_065681.1:p.Arg180Gln
NP_065681.1:p.Arg180Gln
NP_065681.1:p.Arg180Gln
NP_066124.1:p.Arg180Gln
NP_066124.1:p.Arg180Gln
LRG_518t1:c.539G>A
LRG_518t2:c.539G>A
LRG_518:g.30475G>A
LRG_518p1:p.Arg180Gln
LRG_518p2:p.Arg180Gln
NC_000010.10:g.43597991G>A
NM_020630.4:c.539G>A
NM_020630.6:c.539G>A
NM_020975.4:c.539G>A

Protein change:

R137Q

Links:

dbSNP: rs370736139

NCBI 1000 Genomes Browser:

rs370736139

Molecular consequence:

NM_000323.2:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406743.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406744.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406759.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406760.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406761.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406762.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406763.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406764.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406765.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406768.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406769.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406771.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406772.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406773.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406774.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406779.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406780.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406781.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406782.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406783.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406785.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406786.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406787.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020629.2:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020630.7:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020975.6:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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CGA glycoprotein hormones, alpha polypeptide [Homo sapiens]
CGA glycoprotein hormones, alpha polypeptide [Homo sapiens]
Gene ID:1081

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004562535	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Uncertain significance (Sep 11, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004562535

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Uncertain significance
(Sep 11, 2023)

germline

clinical testing

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV004562535.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The RET c.539G>A; p.Arg180Gln variant (rs370736139) is reported in the literature in an individual affected with Hirschsprung disease (Hofstra 2000). This variant is also reported in ClinVar (Variation ID: 161360). This variant is found in the Latino population with an allele frequency of 0.08% (27/35,432 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.223). Due to limited information, the clinical significance of this variant is uncertain at this time. References: Hofstra RM et al. RET and GDNF gene scanning in Hirschsprung patients using two dual denaturing gel systems. Hum Mutat. 2000;15(5):418-29. PMID: 10790203.

#	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: Oct 13, 2024

ClinVar

Relating variation to medicine