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NM_000038.6(APC):c.7201C>T (p.Leu2401=) AND Carcinoma of colon

Germline classification:
Benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001353597.9

Allele description [Variation Report for NM_000038.6(APC):c.7201C>T (p.Leu2401=)]

NM_000038.6(APC):c.7201C>T (p.Leu2401=)

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.7201C>T (p.Leu2401=)
Other names:
CCDS4107.1:c.7201C>T; p.Leu2401Leu
HGVS:
  • NC_000005.10:g.112842795C>T
  • NG_008481.4:g.155275C>T
  • NM_000038.6:c.7201C>TMANE SELECT
  • NM_001127510.3:c.7201C>T
  • NM_001127511.3:c.7147C>T
  • NM_001354895.2:c.7201C>T
  • NM_001354896.2:c.7255C>T
  • NM_001354897.2:c.7231C>T
  • NM_001354898.2:c.7126C>T
  • NM_001354899.2:c.7117C>T
  • NM_001354900.2:c.7078C>T
  • NM_001354901.2:c.7024C>T
  • NM_001354902.2:c.6928C>T
  • NM_001354903.2:c.6898C>T
  • NM_001354904.2:c.6823C>T
  • NM_001354905.2:c.6721C>T
  • NM_001354906.2:c.6352C>T
  • NP_000029.2:p.Leu2401=
  • NP_001120982.1:p.Leu2401=
  • NP_001120983.2:p.Leu2383=
  • NP_001341824.1:p.Leu2401=
  • NP_001341825.1:p.Leu2419=
  • NP_001341826.1:p.Leu2411=
  • NP_001341827.1:p.Leu2376=
  • NP_001341828.1:p.Leu2373=
  • NP_001341829.1:p.Leu2360=
  • NP_001341830.1:p.Leu2342=
  • NP_001341831.1:p.Leu2310=
  • NP_001341832.1:p.Leu2300=
  • NP_001341833.1:p.Leu2275=
  • NP_001341834.1:p.Leu2241=
  • NP_001341835.1:p.Leu2118=
  • LRG_130t1:c.7201C>T
  • LRG_130:g.155275C>T
  • NC_000005.9:g.112178492C>T
  • NM_000038.4:c.7201C>T
  • NM_000038.5:c.7201C>T
  • NM_001127510.2:c.7201C>T
  • c.7201C>T
  • p.L2401L
Links:
dbSNP: rs2229994
NCBI 1000 Genomes Browser:
rs2229994
Molecular consequence:
  • NM_000038.6:c.7201C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.7201C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.7147C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.7201C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.7255C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.7231C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.7126C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.7117C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.7078C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.7024C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.6928C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.6898C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.6823C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.6721C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.6352C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000591206Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591206.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

The p.Leu2401Leu variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located near a splice junction, and is listed in the dbSNP database as coming from a "clinical source" (ID#: rs2229994) with an average heterozygosity of 0.022+/-0.103, therefore increasing the likelihood of this variant to be benign. It has been identified in our laboratory in one among the 973 individuals who have undergone APC testing. Additionally, it has been identified twice in the literature, in 2/258 (0.007% frequency) proband chromosomes and 1/1052 (0.001 frequency) control chromosomes where it was classified as a polymorhism (Hadjisavvas_2006_16650078, Zhou_2004_15122587). In summary, based on the above information, the p.Leu2401Leu variant is classified as predicted benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Nov 3, 2024