NM_020975.6(RET):c.2522C>T (p.Pro841Leu) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 19, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000782197.10

Allele description [Variation Report for NM_020975.6(RET):c.2522C>T (p.Pro841Leu)]

NM_020975.6(RET):c.2522C>T (p.Pro841Leu)

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.2522C>T (p.Pro841Leu)

HGVS:

NC_000010.11:g.43119660C>T
NG_007489.1:g.47592C>T
NM_000323.2:c.2522C>T
NM_001355216.2:c.1760C>T
NM_001406743.1:c.2522C>T
NM_001406744.1:c.2522C>T
NM_001406759.1:c.2522C>T
NM_001406760.1:c.2522C>T
NM_001406761.1:c.2393C>T
NM_001406762.1:c.2393C>T
NM_001406763.1:c.2387C>T
NM_001406764.1:c.2393C>T
NM_001406765.1:c.2387C>T
NM_001406766.1:c.2234C>T
NM_001406767.1:c.2234C>T
NM_001406768.1:c.2258C>T
NM_001406769.1:c.2126C>T
NM_001406770.1:c.2234C>T
NM_001406771.1:c.2084C>T
NM_001406772.1:c.2126C>T
NM_001406773.1:c.2084C>T
NM_001406774.1:c.1997C>T
NM_001406775.1:c.1796C>T
NM_001406776.1:c.1796C>T
NM_001406777.1:c.1796C>T
NM_001406778.1:c.1796C>T
NM_001406779.1:c.1625C>T
NM_001406780.1:c.1625C>T
NM_001406781.1:c.1625C>T
NM_001406782.1:c.1625C>T
NM_001406783.1:c.1496C>T
NM_001406784.1:c.1532C>T
NM_001406785.1:c.1505C>T
NM_001406786.1:c.1496C>T
NM_001406787.1:c.1490C>T
NM_001406788.1:c.1337C>T
NM_001406789.1:c.1337C>T
NM_001406790.1:c.1337C>T
NM_001406791.1:c.1217C>T
NM_001406792.1:c.1073C>T
NM_001406793.1:c.1073C>T
NM_001406794.1:c.1073C>T
NM_020629.2:c.2522C>T
NM_020630.7:c.2522C>T
NM_020975.6:c.2522C>TMANE SELECT
NP_000314.1:p.Pro841Leu
NP_001342145.1:p.Pro587Leu
NP_001342145.1:p.Pro587Leu
NP_001393672.1:p.Pro841Leu
NP_001393673.1:p.Pro841Leu
NP_001393688.1:p.Pro841Leu
NP_001393689.1:p.Pro841Leu
NP_001393690.1:p.Pro798Leu
NP_001393691.1:p.Pro798Leu
NP_001393692.1:p.Pro796Leu
NP_001393693.1:p.Pro798Leu
NP_001393694.1:p.Pro796Leu
NP_001393695.1:p.Pro745Leu
NP_001393696.1:p.Pro745Leu
NP_001393697.1:p.Pro753Leu
NP_001393698.1:p.Pro709Leu
NP_001393699.1:p.Pro745Leu
NP_001393700.1:p.Pro695Leu
NP_001393701.1:p.Pro709Leu
NP_001393702.1:p.Pro695Leu
NP_001393703.1:p.Pro666Leu
NP_001393704.1:p.Pro599Leu
NP_001393705.1:p.Pro599Leu
NP_001393706.1:p.Pro599Leu
NP_001393707.1:p.Pro599Leu
NP_001393708.1:p.Pro542Leu
NP_001393709.1:p.Pro542Leu
NP_001393710.1:p.Pro542Leu
NP_001393711.1:p.Pro542Leu
NP_001393712.1:p.Pro499Leu
NP_001393713.1:p.Pro511Leu
NP_001393714.1:p.Pro502Leu
NP_001393715.1:p.Pro499Leu
NP_001393716.1:p.Pro497Leu
NP_001393717.1:p.Pro446Leu
NP_001393718.1:p.Pro446Leu
NP_001393719.1:p.Pro446Leu
NP_001393720.1:p.Pro406Leu
NP_001393721.1:p.Pro358Leu
NP_001393722.1:p.Pro358Leu
NP_001393723.1:p.Pro358Leu
NP_065680.1:p.Pro841Leu
NP_065681.1:p.Pro841Leu
NP_065681.1:p.Pro841Leu
NP_065681.1:p.Pro841Leu
NP_066124.1:p.Pro841Leu
NP_066124.1:p.Pro841Leu
LRG_518t1:c.2522C>T
LRG_518t2:c.2522C>T
LRG_518:g.47592C>T
LRG_518p1:p.Pro841Leu
LRG_518p2:p.Pro841Leu
NC_000010.10:g.43615108C>T
NM_001355216.1:c.1760C>T
NM_020630.4:c.2522C>T
NM_020630.6:c.2522C>T
NM_020975.4:c.2522C>T

Protein change:

P358L

Links:

dbSNP: rs149891333

NCBI 1000 Genomes Browser:

rs149891333

Molecular consequence:

NM_000323.2:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001355216.2:c.1760C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406743.1:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406744.1:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406759.1:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406760.1:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406761.1:c.2393C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406762.1:c.2393C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406763.1:c.2387C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406764.1:c.2393C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406765.1:c.2387C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406766.1:c.2234C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406767.1:c.2234C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406768.1:c.2258C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406769.1:c.2126C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406770.1:c.2234C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406771.1:c.2084C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406772.1:c.2126C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406773.1:c.2084C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406774.1:c.1997C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406775.1:c.1796C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406776.1:c.1796C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406777.1:c.1796C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406778.1:c.1796C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406779.1:c.1625C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406780.1:c.1625C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406781.1:c.1625C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406782.1:c.1625C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406783.1:c.1496C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406784.1:c.1532C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406785.1:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406786.1:c.1496C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406787.1:c.1490C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406788.1:c.1337C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406789.1:c.1337C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406790.1:c.1337C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406791.1:c.1217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406792.1:c.1073C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406793.1:c.1073C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406794.1:c.1073C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020629.2:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020630.7:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020975.6:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Viburnum opulus var. sargentii chloroplast, complete genome
Viburnum opulus var. sargentii chloroplast, complete genome
gi|2050192922|gb|MT127615.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000920670	Gharavi Laboratory, Columbia University	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 16, 2018)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV004021374	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jul 19, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000920670

Gharavi Laboratory, Columbia University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 16, 2018)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV004021374

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jul 19, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Gharavi Laboratory, Columbia University, SCV000920670.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV004021374.1

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25637381, 24055113, 33219105, 22837065, 21479187, 24134185, 20456320, 26071011, 22648184, 12566528, 14633923, 36251279, 36315513, 29338689, Decker and Peacock_1996)

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

Last Updated: Nov 10, 2024

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