NM_001048174.2(MUTYH):c.196dup (p.Thr66fs) AND Familial adenomatous polyposis 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 24, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003331739.1

Allele description [Variation Report for NM_001048174.2(MUTYH):c.196dup (p.Thr66fs)]

NM_001048174.2(MUTYH):c.196dup (p.Thr66fs)

Gene:

MUTYH:mutY DNA glycosylase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1p34.1

Genomic location:

Preferred name:

NM_001048174.2(MUTYH):c.196dup (p.Thr66fs)

HGVS:

NC_000001.11:g.45333481dup
NG_008189.1:g.11990dup
NM_001048171.2:c.196dup
NM_001048172.2:c.199dup
NM_001048173.2:c.196dup
NM_001048174.2:c.196dupMANE SELECT
NM_001128425.2:c.280dup
NM_001293190.2:c.241dup
NM_001293191.2:c.229dup
NM_001293192.2:c.-81dup
NM_001293195.2:c.196dup
NM_001293196.2:c.-81dup
NM_001350650.2:c.-76dup
NM_001350651.2:c.-76dup
NM_001407069.1:c.271dup
NM_001407070.1:c.196dup
NM_001407071.1:c.199dup
NM_001407072.1:c.196dup
NM_001407073.1:c.238dup
NM_001407075.1:c.112dup
NM_001407077.1:c.229dup
NM_001407078.1:c.199dup
NM_001407079.1:c.199dup
NM_001407080.1:c.196dup
NM_001407081.1:c.196dup
NM_001407082.1:c.-76dup
NM_001407083.1:c.238dup
NM_001407085.1:c.238dup
NM_001407086.1:c.199dup
NM_001407087.1:c.217dup
NM_001407088.1:c.196dup
NM_001407089.1:c.196dup
NM_001407091.1:c.-81dup
NM_012222.3:c.271dup
NP_001041636.2:p.Thr66fs
NP_001041637.1:p.Thr67fs
NP_001041638.1:p.Thr66fs
NP_001041639.1:p.Thr66fs
NP_001121897.1:p.Thr94Asnfs
NP_001121897.1:p.Thr94fs
NP_001280119.1:p.Thr81fs
NP_001280120.1:p.Thr77fs
NP_001280124.1:p.Thr66fs
NP_001393998.1:p.Thr91fs
NP_001393999.1:p.Thr66fs
NP_001394000.1:p.Thr67fs
NP_001394001.1:p.Thr66fs
NP_001394002.1:p.Thr80fs
NP_001394004.1:p.Thr38fs
NP_001394006.1:p.Thr77fs
NP_001394007.1:p.Thr67fs
NP_001394008.1:p.Thr67fs
NP_001394009.1:p.Thr66fs
NP_001394010.1:p.Thr66fs
NP_001394012.1:p.Thr80fs
NP_001394014.1:p.Thr80fs
NP_001394015.1:p.Thr67fs
NP_001394016.1:p.Thr73fs
NP_001394017.1:p.Thr66fs
NP_001394018.1:p.Thr66fs
NP_036354.1:p.Thr91fs
LRG_220t1:c.280dup
LRG_220:g.11990dup
LRG_220p1:p.Thr94Asnfs
NC_000001.10:g.45799153dup
NM_001128425.1:c.280dup
NM_001128425.1:c.280dupA
NR_146882.2:n.424dup
NR_146883.2:n.347dup
NR_176269.1:n.420dup
NR_176270.1:n.360dup
NR_176271.1:n.283dup
NR_176272.1:n.347dup
NR_176273.1:n.347dup
NR_176274.1:n.360dup

Protein change:

T38fs

Molecular consequence:

NM_001293192.2:c.-81dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001293196.2:c.-81dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350650.2:c.-76dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350651.2:c.-76dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407082.1:c.-76dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407091.1:c.-81dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001048171.2:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001048172.2:c.199dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001048173.2:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001048174.2:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001128425.2:c.280dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001293190.2:c.241dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001293191.2:c.229dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001293195.2:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407069.1:c.271dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407070.1:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407071.1:c.199dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407072.1:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407073.1:c.238dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407075.1:c.112dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407077.1:c.229dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407078.1:c.199dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407079.1:c.199dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407080.1:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407081.1:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407083.1:c.238dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407085.1:c.238dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407086.1:c.199dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407087.1:c.217dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407088.1:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407089.1:c.196dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012222.3:c.271dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_146882.2:n.424dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146883.2:n.347dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176269.1:n.420dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176271.1:n.283dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176272.1:n.347dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176273.1:n.347dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176274.1:n.360dup - 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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Homo sapiens YY2 transcription factor (YY2), mRNA
Homo sapiens YY2 transcription factor (YY2), mRNA
gi|1653962491|ref|NM_206923.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004039294	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Aug 24, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004039294

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Aug 24, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004039294.1

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

Description

Variant summary: MUTYH c.280dupA (p.Thr94AsnfsX27) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251492 control chromosomes (gnomAD). To our knowledge, no occurrence of c.280dupA in individuals affected with MUTYH-Associated Polyposis and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.

#	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: Oct 7, 2023

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