NM_001128425.1(MUTYH):c.1090C>T (p.Arg364Cys) AND Hereditary cancer-predisposing syndrome

Clinical significance:Uncertain significance (Last evaluated: Oct 12, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000223437.8

Allele description [Variation Report for NM_001128425.1(MUTYH):c.1090C>T (p.Arg364Cys)]

NM_001128425.1(MUTYH):c.1090C>T (p.Arg364Cys)

Gene:
MUTYH:mutY DNA glycosylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_001128425.1(MUTYH):c.1090C>T (p.Arg364Cys)
HGVS:
  • NC_000001.11:g.45331757G>A
  • NG_008189.1:g.13714C>T
  • NM_001048171.1:c.1048C>T
  • NM_001048172.1:c.1009C>T
  • NM_001048173.1:c.1006C>T
  • NM_001048174.1:c.1006C>T
  • NM_001128425.1:c.1090C>T
  • NM_001293190.1:c.1051C>T
  • NM_001293191.1:c.1039C>T
  • NM_001293192.1:c.730C>T
  • NM_001293195.1:c.1006C>T
  • NM_001293196.1:c.730C>T
  • NM_001350650.1:c.661C>T
  • NM_001350651.1:c.661C>T
  • NM_012222.2:c.1081C>T
  • NP_001041636.1:p.Arg350Cys
  • NP_001041637.1:p.Arg337Cys
  • NP_001041638.1:p.Arg336Cys
  • NP_001041639.1:p.Arg336Cys
  • NP_001121897.1:p.Arg364Cys
  • NP_001280119.1:p.Arg351Cys
  • NP_001280120.1:p.Arg347Cys
  • NP_001280121.1:p.Arg244Cys
  • NP_001280124.1:p.Arg336Cys
  • NP_001280125.1:p.Arg244Cys
  • NP_001337579.1:p.Arg221Cys
  • NP_001337580.1:p.Arg221Cys
  • NP_036354.1:p.Arg361Cys
  • LRG_220t1:c.1090C>T
  • LRG_220:g.13714C>T
  • LRG_220p1:p.Arg364Cys
  • NC_000001.10:g.45797429G>A
  • NR_146882.1:n.1264C>T
  • NR_146883.1:n.1078C>T
Protein change:
R221C
Links:
dbSNP: rs151316420
NCBI 1000 Genomes Browser:
rs151316420
Molecular consequence:
  • NM_001048171.1:c.1048C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001048172.1:c.1009C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001048173.1:c.1006C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001048174.1:c.1006C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128425.1:c.1090C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001293190.1:c.1051C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001293191.1:c.1039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001293192.1:c.730C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001293195.1:c.1006C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001293196.1:c.730C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350650.1:c.661C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350651.1:c.661C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_012222.2:c.1081C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146882.1:n.1264C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146883.1:n.1078C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MedGen: C0027672

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000274900Ambry Geneticscriteria provided, single submitter
Uncertain significance
(May 12, 2020)
germlineclinical testing

Citation Link,

SCV000685538Color Health, Inccriteria provided, single submitter
Uncertain significance
(Oct 12, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Ambry Genetics, SCV000274900.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The p.R364C variant (also known as c.1090C>T), located in coding exon 12 of the MUTYH gene, results from a C to T substitution at nucleotide position 1090. The arginine at codon 364 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

From Color Health, Inc, SCV000685538.4

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

Description

This missense variant replaces arginine with cysteine at codon 364 of the MUTYH protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 2/249872 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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

Last Updated: Jun 25, 2021

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