NM_001048174.2(MUTYH):c.262C>G (p.Arg88Gly) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 5, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001020376.6

Allele description [Variation Report for NM_001048174.2(MUTYH):c.262C>G (p.Arg88Gly)]

NM_001048174.2(MUTYH):c.262C>G (p.Arg88Gly)

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.262C>G (p.Arg88Gly)

HGVS:

NC_000001.11:g.45333415G>C
NG_008189.1:g.12056C>G
NM_001048171.2:c.262C>G
NM_001048172.2:c.265C>G
NM_001048173.2:c.262C>G
NM_001048174.2:c.262C>GMANE SELECT
NM_001128425.2:c.346C>G
NM_001293190.2:c.307C>G
NM_001293191.2:c.295C>G
NM_001293192.2:c.-15C>G
NM_001293195.2:c.262C>G
NM_001293196.2:c.-15C>G
NM_001350650.2:c.-10C>G
NM_001350651.2:c.-10C>G
NM_012222.3:c.337C>G
NP_001041636.2:p.Arg88Gly
NP_001041637.1:p.Arg89Gly
NP_001041638.1:p.Arg88Gly
NP_001041639.1:p.Arg88Gly
NP_001121897.1:p.Arg116Gly
NP_001280119.1:p.Arg103Gly
NP_001280120.1:p.Arg99Gly
NP_001280124.1:p.Arg88Gly
NP_036354.1:p.Arg113Gly
LRG_220t1:c.346C>G
LRG_220:g.12056C>G
NC_000001.10:g.45799087G>C
NM_001128425.1:c.346C>G
NR_146882.2:n.490C>G
NR_146883.2:n.413C>G

Protein change:

R103G

Links:

dbSNP: rs373766973

NCBI 1000 Genomes Browser:

rs373766973

Molecular consequence:

NM_001293192.2:c.-15C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001293196.2:c.-15C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350650.2:c.-10C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350651.2:c.-10C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001048171.2:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001048172.2:c.265C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001048173.2:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001048174.2:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001128425.2:c.346C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001293190.2:c.307C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001293191.2:c.295C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001293195.2:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_012222.3:c.337C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_146882.2:n.490C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146883.2:n.413C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001181849	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 5, 2023)	germline	clinical testing	Citation Link,
SCV001358939	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 1, 2021)	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

SCV001181849

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 5, 2023)

germline

clinical testing

Citation Link,

SCV001358939

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 1, 2021)

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

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, SCV001181849.4

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

Description

The p.R116G variant (also known as c.346C>G), located in coding exon 3 of the MUTYH gene, results from a C to G substitution at nucleotide position 346. The arginine at codon 116 is replaced by glycine, an amino acid with dissimilar properties. This nucleotide position is not well conserved in available vertebrate species. This amino acid position is not well conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive; however, direct evidence is insufficient at this time (Ambry internal data). In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

From Color Diagnostics, LLC DBA Color Health, SCV001358939.2

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

Description

This missense variant replaces arginine with glycine at codon 116 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 not been identified 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.

#	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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