NM_002691.4(POLD1):c.885_887del (p.Val296del) AND Colorectal cancer, susceptibility to, 10

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 23, 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:: RCV000462957.5

Allele description [Variation Report for NM_002691.4(POLD1):c.885_887del (p.Val296del)]

NM_002691.4(POLD1):c.885_887del (p.Val296del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_002691.4(POLD1):c.885_887del (p.Val296del)

HGVS:

NC_000019.10:g.50402656_50402658del
NC_000019.9:g.50905911_50905913del
NG_033800.1:g.23334_23336del
NM_001256849.1:c.885_887del
NM_001308632.1:c.885_887del
NM_002691.4:c.885_887delMANE SELECT
NP_001243778.1:p.Val296del
NP_001295561.1:p.Val296del
NP_002682.2:p.Val296del
LRG_785t1:c.885_887del
LRG_785t2:c.885_887del
LRG_785:g.23334_23336del
LRG_785p1:p.Val296del
LRG_785p2:p.Val296del
NC_000019.9:g.50905911_50905913del
NC_000019.9:g.50905911_50905913delGTG
NC_000019.9:g.50905913_50905915del
NM_002691.3:c.885_887del
NM_002691.3:c.885_887delGGT
NR_046402.2:n.930_932del

Protein change:

V296del

Links:

dbSNP: rs1060501809

NCBI 1000 Genomes Browser:

rs1060501809

Molecular consequence:

NM_001256849.1:c.885_887del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001308632.1:c.885_887del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002691.4:c.885_887del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_046402.2:n.930_932del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000547524	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 23, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000547524

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 23, 2016)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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, SCV000547524.5

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

Description

In summary, this variant is a novel single amino acid deletion with uncertain impact on mRNA splicing and protein function. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on mRNA splicing suggest that this variant may alter mRNA splicing, but this prediction has not been confirmed by published transcriptional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a POLD1-related disease. This sequence change deletes 3 nucleotides from exon 8 of the POLD1 mRNA (c.885_887delGGT). This leads to the deletion of 1 amino acid residue in the POLD1 protein (p.Val296del) but otherwise preserves the integrity of the reading frame.

#	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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