NM_002691.4(POLD1):c.946G>A (p.Asp316Asn) AND Colorectal cancer, susceptibility to, 10

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 29, 2024
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:: RCV000699256.6

Allele description [Variation Report for NM_002691.4(POLD1):c.946G>A (p.Asp316Asn)]

NM_002691.4(POLD1):c.946G>A (p.Asp316Asn)

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.946G>A (p.Asp316Asn)

HGVS:

NC_000019.10:g.50402717G>A
NG_033800.1:g.23395G>A
NM_001256849.1:c.946G>A
NM_001308632.1:c.946G>A
NM_002691.4:c.946G>AMANE SELECT
NP_001243778.1:p.Asp316Asn
NP_001295561.1:p.Asp316Asn
NP_002682.2:p.Asp316Asn
LRG_785t1:c.946G>A
LRG_785t2:c.946G>A
LRG_785:g.23395G>A
LRG_785p1:p.Asp316Asn
LRG_785p2:p.Asp316Asn
NC_000019.9:g.50905974G>A
NM_002691.2:c.946G>A
NM_002691.3:c.946G>A
NR_046402.2:n.991G>A

Protein change:

D316N

Links:

dbSNP: rs746087148

NCBI 1000 Genomes Browser:

rs746087148

Molecular consequence:

NM_001256849.1:c.946G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001308632.1:c.946G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002691.4:c.946G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046402.2:n.991G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Colorectal cancer, susceptibility to, 10
Synonyms:: COLORECTAL CANCER, SUSCEPTIBILITY TO, ON CHROMOSOME 19q; Colorectal cancer 10
Identifiers:: MONDO: MONDO:0012953; MedGen: C2675481; Orphanet: 220460; OMIM: 612591

Recent activity

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microtubule-associated serine/threonine-protein kinase 2 isoform X26 [Homo sapie...
microtubule-associated serine/threonine-protein kinase 2 isoform X26 [Homo sapiens]
gi|2462506597|ref|XP_054191329.1|

Protein
Taxonomy Links for GEO Profiles (Select 101677630) (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000827958	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 29, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19282447, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000827958

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 29, 2024)

germline

clinical testing

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

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

Proofreading exonuclease activity of human DNA polymerase delta and its effects on lesion-bypass DNA synthesis.

Fazlieva R, Spittle CS, Morrissey D, Hayashi H, Yan H, Matsumoto Y.

Nucleic Acids Res. 2009 May;37(9):2854-66. doi: 10.1093/nar/gkp155. Epub 2009 Mar 12.

PubMed [citation]

PMID:: 19282447
PMCID:: PMC2685094

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000827958.5

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 316 of the POLD1 protein (p.Asp316Asn). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with POLD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 246506). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt POLD1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects POLD1 function (PMID: 19282447). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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