NM_001048174.2(MUTYH):c.32G>A (p.Gly11Asp) AND Familial adenomatous polyposis 2

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Feb 1, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000123155.32

Allele description [Variation Report for NM_001048174.2(MUTYH):c.32G>A (p.Gly11Asp)]

NM_001048174.2(MUTYH):c.32G>A (p.Gly11Asp)

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.32G>A (p.Gly11Asp)

Other names:

p.G25D:GGT>GAT

HGVS:

NC_000001.11:g.45334474C>T
NG_008189.1:g.10997G>A
NM_001048171.2:c.32G>A
NM_001048172.2:c.32G>A
NM_001048173.2:c.32G>A
NM_001048174.2:c.32G>AMANE SELECT
NM_001128425.2:c.74G>A
NM_001293190.2:c.74G>A
NM_001293191.2:c.32G>A
NM_001293192.2:c.-181G>A
NM_001293195.2:c.32G>A
NM_001293196.2:c.-181G>A
NM_001350650.2:c.-240G>A
NM_001350651.2:c.-176G>A
NM_012222.3:c.74G>A
NP_001041636.1:p.Gly25Asp
NP_001041636.2:p.Gly11Asp
NP_001041637.1:p.Gly11Asp
NP_001041638.1:p.Gly11Asp
NP_001041639.1:p.Gly11Asp
NP_001121897.1:p.Gly25Asp
NP_001121897.1:p.Gly25Asp
NP_001280119.1:p.Gly25Asp
NP_001280120.1:p.Gly11Asp
NP_001280124.1:p.Gly11Asp
NP_036354.1:p.Gly25Asp
NP_036354.1:p.Gly25Asp
LRG_220t1:c.74G>A
LRG_220:g.10997G>A
LRG_220p1:p.Gly25Asp
NC_000001.10:g.45800146C>T
NM_001048171.1:c.74G>A
NM_001128425.1:c.74G>A
NM_012222.2:c.74G>A
NR_146882.2:n.260G>A
NR_146883.2:n.183G>A
p.G25D

Protein change:

G11D

Links:

dbSNP: rs75321043

NCBI 1000 Genomes Browser:

rs75321043

Molecular consequence:

NM_001293192.2:c.-181G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001293196.2:c.-181G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350650.2:c.-240G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350651.2:c.-176G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001048171.2:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001048172.2:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001048173.2:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001048174.2:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128425.2:c.74G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293190.2:c.74G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293191.2:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001293195.2:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_012222.3:c.74G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_146882.2:n.260G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146883.2:n.183G>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
SCV000166459	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000267405	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 18422726, 25741868
SCV000788437	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Nov 13, 2017)	unknown	clinical testing	PubMed (14) [See all records that cite these PMIDs] 18422726, 25820570, 26332594, 24728327, 25186627, 18811933, 17703316, 22641385, 16929514, 17252231, 25980754, 26684191, 27443514, 22703879 Citation Link,
SCV001135267	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001257715	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	Citation Link

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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
East Asian	germline	unknown	4	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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

See all PubMed Citations (16)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000166459.13

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267405.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	4	not provided	not provided	reference population	PubMed (2)

#	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		4	not provided	not provided	not provided

From Counsyl, SCV000788437.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (14)

#	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

From Mendelics, SCV001135267.1

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

#	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

From Illumina Laboratory Services, Illumina, SCV001257715.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown 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: Nov 3, 2024

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