NM_002691.4(POLD1):c.521G>A (p.Arg174Gln) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Nov 21, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000679519.37

Allele description [Variation Report for NM_002691.4(POLD1):c.521G>A (p.Arg174Gln)]

NM_002691.4(POLD1):c.521G>A (p.Arg174Gln)

Gene:

POLD1:DNA polymerase delta 1, catalytic subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_002691.4(POLD1):c.521G>A (p.Arg174Gln)

HGVS:

NC_000019.10:g.50402056G>A
NG_033800.1:g.22734G>A
NM_001256849.1:c.521G>A
NM_001308632.1:c.521G>A
NM_002691.4:c.521G>AMANE SELECT
NP_001243778.1:p.Arg174Gln
NP_001295561.1:p.Arg174Gln
NP_002682.2:p.Arg174Gln
LRG_785t1:c.521G>A
LRG_785t2:c.521G>A
LRG_785:g.22734G>A
LRG_785p1:p.Arg174Gln
LRG_785p2:p.Arg174Gln
NC_000019.9:g.50905313G>A
NM_001308632.1:c.521G>A
NM_002691.2:c.521G>A
NM_002691.3:c.521G>A
NR_046402.2:n.566G>A

Protein change:

R174Q

Links:

dbSNP: rs141976385

NCBI 1000 Genomes Browser:

rs141976385

Molecular consequence:

NM_001256849.1:c.521G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001308632.1:c.521G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002691.4:c.521G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046402.2:n.566G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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uncharacterized protein AT2G16270 [Arabidopsis thaliana]
uncharacterized protein AT2G16270 [Arabidopsis thaliana]
gi|15226723|ref|NP_179222.1|

Protein
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein [Arabid...
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein [Arabidopsis thaliana]
gi|30679168|ref|NP_851026.1|

Protein
Plant sample from Coula edulis
Plant sample from Coula edulis

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000293592	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Nov 21, 2023)	germline	clinical testing	Citation Link,
SCV000806547	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 8, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000888467	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Nov 3, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001152015	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Mar 1, 2021)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000293592.13

#	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 does not alter protein structure/function; Observed in an individual with breast cancer (PMID: 35264596); This variant is associated with the following publications: (PMID: 30061258, 35264596)

#	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

From PreventionGenetics, part of Exact Sciences, SCV000806547.1

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

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000888467.2

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001152015.27

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

#	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		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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