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NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=) AND Carcinoma of colon

Germline classification:
Likely 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:
RCV001355953.1

Allele description [Variation Report for NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=)]

NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=)

Gene:
MUTYH:mutY DNA glycosylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=)
HGVS:
  • NC_000001.11:g.45331194G>A
  • NG_008189.1:g.14277C>T
  • NM_001048171.2:c.1380C>T
  • NM_001048172.2:c.1383C>T
  • NM_001048173.2:c.1380C>T
  • NM_001048174.2:c.1380C>TMANE SELECT
  • NM_001128425.2:c.1464C>T
  • NM_001293190.2:c.1425C>T
  • NM_001293191.2:c.1413C>T
  • NM_001293192.2:c.1104C>T
  • NM_001293195.2:c.1380C>T
  • NM_001293196.2:c.1104C>T
  • NM_001350650.2:c.1035C>T
  • NM_001350651.2:c.1035C>T
  • NM_012222.3:c.1455C>T
  • NP_001041636.2:p.Thr460=
  • NP_001041637.1:p.Thr461=
  • NP_001041638.1:p.Thr460=
  • NP_001041639.1:p.Thr460=
  • NP_001121897.1:p.Thr488=
  • NP_001121897.1:p.Thr488=
  • NP_001280119.1:p.Thr475=
  • NP_001280120.1:p.Thr471=
  • NP_001280121.1:p.Thr368=
  • NP_001280124.1:p.Thr460=
  • NP_001280125.1:p.Thr368=
  • NP_001337579.1:p.Thr345=
  • NP_001337580.1:p.Thr345=
  • NP_036354.1:p.Thr485=
  • LRG_220t1:c.1464C>T
  • LRG_220:g.14277C>T
  • LRG_220p1:p.Thr488=
  • NC_000001.10:g.45796866G>A
  • NM_001128425.1:c.1464C>T
  • NR_146882.2:n.1608C>T
  • NR_146883.2:n.1457C>T
  • p.T488T
Links:
dbSNP: rs373973053
NCBI 1000 Genomes Browser:
rs373973053
Molecular consequence:
  • NR_146882.2:n.1608C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146883.2:n.1457C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001048171.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001048172.2:c.1383C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001048173.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001048174.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001128425.2:c.1464C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001293190.2:c.1425C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001293191.2:c.1413C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001293192.2:c.1104C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001293195.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001293196.2:c.1104C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001350650.2:c.1035C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001350651.2:c.1035C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_012222.3:c.1455C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

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
SCV001550986Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not 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), SCV001550986.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The MUTYH p.Thr488= variant was not identified in the literature nor was it identified in the GeneInsight-COGR, Cosmic, or UMD-LSDB, databases. The variant was identified in dbSNP (ID: rs373973053) as "With Likely benign allele ", and in ClinVar database (classified as likely benign by Ambry Genetics, Invitae, GeneDx, and Color Genomics). The variant was identified in control databases in 5 of 246234 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Latino in 3 of 33582 chromosomes (freq: 0.00009), European in 1 of 111694 chromosomes (freq: 0.000009), East Asian in 1 of 17248 chromosomes (freq: 0.00006), while the variant was not observed in the African, Other, Ashkenazi Jewish, Finnish, and South Asian populations. The p.Thr488= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024