NM_001048174.2(MUTYH):c.1534G>A (p.Asp512Asn) AND Familial adenomatous polyposis 2

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 24, 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:: RCV001059206.10

Allele description [Variation Report for NM_001048174.2(MUTYH):c.1534G>A (p.Asp512Asn)]

NM_001048174.2(MUTYH):c.1534G>A (p.Asp512Asn)

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.1534G>A (p.Asp512Asn)

HGVS:

NC_000001.11:g.45329338C>T
NG_008189.1:g.16133G>A
NM_001048171.2:c.1534G>A
NM_001048172.2:c.1537G>A
NM_001048173.2:c.1534G>A
NM_001048174.2:c.1534G>AMANE SELECT
NM_001128425.2:c.1618G>A
NM_001293190.2:c.1579G>A
NM_001293191.2:c.1567G>A
NM_001293192.2:c.1258G>A
NM_001293195.2:c.1534G>A
NM_001293196.2:c.1258G>A
NM_001350650.2:c.1189G>A
NM_001350651.2:c.1189G>A
NM_012222.3:c.1609G>A
NP_001041636.2:p.Asp512Asn
NP_001041637.1:p.Asp513Asn
NP_001041638.1:p.Asp512Asn
NP_001041639.1:p.Asp512Asn
NP_001121897.1:p.Asp540Asn
NP_001121897.1:p.Asp540Asn
NP_001280119.1:p.Asp527Asn
NP_001280120.1:p.Asp523Asn
NP_001280121.1:p.Asp420Asn
NP_001280124.1:p.Asp512Asn
NP_001280125.1:p.Asp420Asn
NP_001337579.1:p.Asp397Asn
NP_001337580.1:p.Asp397Asn
NP_036354.1:p.Asp537Asn
LRG_220t1:c.1618G>A
LRG_220:g.16133G>A
LRG_220p1:p.Asp540Asn
NC_000001.10:g.45795010C>T
NM_001128425.1:c.1618G>A
NR_146882.2:n.1942G>A
NR_146883.2:n.1791G>A

Protein change:

D397N

Links:

dbSNP: rs1439243449

NCBI 1000 Genomes Browser:

rs1439243449

Molecular consequence:

NM_001048171.2:c.1534G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001048172.2:c.1537G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001048173.2:c.1534G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001048174.2:c.1534G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128425.2:c.1618G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293190.2:c.1579G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293191.2:c.1567G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293192.2:c.1258G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293195.2:c.1534G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293196.2:c.1258G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001350650.2:c.1189G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001350651.2:c.1189G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_012222.3:c.1609G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_146882.2:n.1942G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146883.2:n.1791G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Familial adenomatous polyposis 2
Synonyms:: COLORECTAL ADENOMATOUS POLYPOSIS, AUTOSOMAL RECESSIVE; ADENOMAS, MULTIPLE COLORECTAL, AUTOSOMAL RECESSIVE; MYH-associated polyposis; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012041; MedGen: C3272841; Orphanet: 220460; OMIM: 608456

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001223823	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004198942	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 31, 2023)	unknown	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

SCV001223823

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 24, 2023)

germline

clinical testing

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

SCV004198942

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 31, 2023)

unknown

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Nothing to display

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001223823.5

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 540 of the MUTYH protein (p.Asp540Asn). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with MUTYH-related conditions. ClinVar contains an entry for this variant (Variation ID: 492027). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. 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.

#	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 Baylor Genetics, SCV004198942.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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