NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=) AND Familial adenomatous polyposis 2

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Jan 13, 2024
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:: RCV000225914.15

Allele description [Variation Report for NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=)]

NM_001048174.2(MUTYH):c.1380C>T (p.Thr460=)

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.1380C>T (p.Thr460=)

HGVS:

NC_000001.11:g.45331194G>A
NG_008189.1:g.14277C>T
NM_001048171.2:c.1380C>T
NM_001048172.2:c.1383C>T
NM_001048173.2:c.1380C>T
NM_001048174.2:c.1380C>TMANE SELECT
NM_001128425.2:c.1464C>T
NM_001293190.2:c.1425C>T
NM_001293191.2:c.1413C>T
NM_001293192.2:c.1104C>T
NM_001293195.2:c.1380C>T
NM_001293196.2:c.1104C>T
NM_001350650.2:c.1035C>T
NM_001350651.2:c.1035C>T
NM_012222.3:c.1455C>T
NP_001041636.2:p.Thr460=
NP_001041637.1:p.Thr461=
NP_001041638.1:p.Thr460=
NP_001041639.1:p.Thr460=
NP_001121897.1:p.Thr488=
NP_001121897.1:p.Thr488=
NP_001280119.1:p.Thr475=
NP_001280120.1:p.Thr471=
NP_001280121.1:p.Thr368=
NP_001280124.1:p.Thr460=
NP_001280125.1:p.Thr368=
NP_001337579.1:p.Thr345=
NP_001337580.1:p.Thr345=
NP_036354.1:p.Thr485=
LRG_220t1:c.1464C>T
LRG_220:g.14277C>T
LRG_220p1:p.Thr488=
NC_000001.10:g.45796866G>A
NM_001128425.1:c.1464C>T
NR_146882.2:n.1608C>T
NR_146883.2:n.1457C>T
p.T488T

Links:

dbSNP: rs373973053

NCBI 1000 Genomes Browser:

rs373973053

Molecular consequence:

NR_146882.2:n.1608C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146883.2:n.1457C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001048171.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001048172.2:c.1383C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001048173.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001048174.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001128425.2:c.1464C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001293190.2:c.1425C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001293191.2:c.1413C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001293192.2:c.1104C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001293195.2:c.1380C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001293196.2:c.1104C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350650.2:c.1035C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350651.2:c.1035C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_012222.3:c.1455C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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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Gene ID:26433

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000285931	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 13, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004016031	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004831757	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Nov 30, 2023)	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

SCV000285931

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 13, 2024)

germline

clinical testing

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

SCV004016031

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 7, 2023)

germline

clinical testing

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

SCV004831757

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Nov 30, 2023)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	108544	not provided	clinical testing

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000285931.9

#	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 KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004016031.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From All of Us Research Program, National Institutes of Health, SCV004831757.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	108544	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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