NM_002691.4(POLD1):c.1562G>A (p.Arg521Gln) AND Colorectal cancer

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 1, 2016
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:: RCV000590937.3

Allele description [Variation Report for NM_002691.4(POLD1):c.1562G>A (p.Arg521Gln)]

NM_002691.4(POLD1):c.1562G>A (p.Arg521Gln)

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.1562G>A (p.Arg521Gln)

HGVS:

NC_000019.10:g.50407050G>A
NG_033800.1:g.27728G>A
NM_001256849.1:c.1562G>A
NM_001308632.1:c.1562G>A
NM_002691.4:c.1562G>AMANE SELECT
NP_001243778.1:p.Arg521Gln
NP_001295561.1:p.Arg521Gln
NP_002682.2:p.Arg521Gln
LRG_785t1:c.1562G>A
LRG_785t2:c.1562G>A
LRG_785:g.27728G>A
LRG_785p1:p.Arg521Gln
LRG_785p2:p.Arg521Gln
NC_000019.9:g.50910307G>A
NM_002691.2:c.1562G>A
NM_002691.3:c.1562G>A
NM_002691.4:c.1562G>A
NR_046402.2:n.1607G>A

Protein change:

R521Q

Links:

dbSNP: rs143076166

NCBI 1000 Genomes Browser:

rs143076166

Molecular consequence:

NM_001256849.1:c.1562G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001308632.1:c.1562G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002691.4:c.1562G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046402.2:n.1607G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Colorectal cancer
Synonyms:: Colorectal cancer, somatic; Malignant Colorectal Neoplasm
Identifiers:: MONDO: MONDO:0005575; MedGen: C0346629; OMIM: 114500

Recent activity

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The CHARGE syndrome ortholog CHD-7 regulates TGF-b pathways in C. elegans
The CHARGE syndrome ortholog CHD-7 regulates TGF-b pathways in C. elegans
The CHARGE syndrome ortholog CHD-7 regulates TGF-b pathways in C. elegans

BioProject
JGI_CAAK1338.rev NIH_XGC_tropBrn3 Xenopus tropicalis cDNA clone IMAGE:7652329 3'...
JGI_CAAK1338.rev NIH_XGC_tropBrn3 Xenopus tropicalis cDNA clone IMAGE:7652329 3', mRNA sequence
gi|58370019|gnl|dbEST|27507607|gb|C 92.1|

Nucleotide
LOC121321479 [Polyodon spathula]
LOC121321479 [Polyodon spathula]
Gene ID:121321479

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000700093	CSER _CC_NCGL, University of Washington - CSER - NEXT Medicine variant annotation	criteria provided, single submitter (Amendola et al. (Genome Res. 2015))	Uncertain significance (Oct 1, 2016)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000700093

CSER _CC_NCGL, University of Washington - CSER - NEXT Medicine variant annotation

criteria provided, single submitter

(Amendola et al. (Genome Res. 2015))

Uncertain significance
(Oct 1, 2016)

germline

research

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

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	research

Citations

PubMed

Actionable exomic incidental findings in 6503 participants: challenges of variant classification.

Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, et al.

Genome Res. 2015 Mar;25(3):305-15. doi: 10.1101/gr.183483.114. Epub 2015 Jan 30.

PubMed [citation]

PMID:: 25637381
PMCID:: PMC4352885

Details of each submission

From CSER _CC_NCGL, University of Washington - CSER - NEXT Medicine variant annotation, SCV000700093.1

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

Description

Found in patient having exome sequencing due to suspicion for hereditary colon cancer and/or polyps. Patient is a 37 year old female diagnosed with colon cancer at age 36. Patient also has a likely pathogenic variant in MSH2. This interpretation considers GERP score and allele frequency data, in addition to published reports of the variant in the literature, available at the time of review.

#	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: Oct 8, 2024

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