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NM_002691.4(POLD1):c.1692G>C (p.Met564Ile) AND Colorectal cancer, susceptibility to, 10

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 9, 2023
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:
RCV001992172.6

Allele description [Variation Report for NM_002691.4(POLD1):c.1692G>C (p.Met564Ile)]

NM_002691.4(POLD1):c.1692G>C (p.Met564Ile)

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.1692G>C (p.Met564Ile)
HGVS:
  • NC_000019.10:g.50407332G>C
  • NG_033800.1:g.28010G>C
  • NM_001256849.1:c.1692G>C
  • NM_001308632.1:c.1692G>C
  • NM_002691.4:c.1692G>CMANE SELECT
  • NP_001243778.1:p.Met564Ile
  • NP_001295561.1:p.Met564Ile
  • NP_002682.2:p.Met564Ile
  • LRG_785t1:c.1692G>C
  • LRG_785t2:c.1692G>C
  • LRG_785:g.28010G>C
  • LRG_785p1:p.Met564Ile
  • LRG_785p2:p.Met564Ile
  • NC_000019.9:g.50910589G>C
  • NR_046402.2:n.1737G>C
Protein change:
M564I
Links:
dbSNP: rs544143880
NCBI 1000 Genomes Browser:
rs544143880
Molecular consequence:
  • NM_001256849.1:c.1692G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001308632.1:c.1692G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002691.4:c.1692G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_046402.2:n.1737G>C - 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

  • txid7955[organism] AND (cd2ap[gene symbol] OR (BC086846 OR BC0868... (20)
    txid7955[organism] AND (cd2ap[gene symbol] OR (BC086846 OR BC086846.* OR BC164631 OR BC164631.* OR AW280139 OR AW280139.* OR AW281166 OR AW281166.* OR CK690519 OR CK690519.* OR BC086846 OR BC086846.* OR BC164631 OR BC164631.* OR CK690519 OR CK690519.* OR DT075242 OR DT075242.* OR DT081164 OR DT081164.* OR EB864755 OR EB864755.* OR GDQH01003029 OR GDQH01003029.* OR GFIL01003436 OR GFIL01003436.* OR NM_001008583 OR NM_001008583.* OR XM_005160684 OR XM_005160684.* OR XM_009294709 OR XM_009294709.*))
    Search
    GEO Profiles
  • Desmodium lilloanum (0)
    Taxonomy
  • expansin-A9-like [Cucurbita maxima]
    expansin-A9-like [Cucurbita maxima]
    gi|1280988983|ref|XP_022977999.1|
    Protein

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002284361Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Aug 9, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002284361.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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 not expected to disrupt POLD1 protein function. 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. ClinVar contains an entry for this variant (Variation ID: 1496994). This variant has not been reported in the literature in individuals affected with POLD1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 564 of the POLD1 protein (p.Met564Ile).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024