NM_001048174.2(MUTYH):c.916C>T (p.Pro306Ser) AND Familial adenomatous polyposis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 2, 2024
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:: RCV000820649.8

Allele description [Variation Report for NM_001048174.2(MUTYH):c.916C>T (p.Pro306Ser)]

NM_001048174.2(MUTYH):c.916C>T (p.Pro306Ser)

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.916C>T (p.Pro306Ser)

HGVS:

NC_000001.11:g.45331847G>A
NG_008189.1:g.13624C>T
NM_001048171.2:c.916C>T
NM_001048172.2:c.919C>T
NM_001048173.2:c.916C>T
NM_001048174.2:c.916C>TMANE SELECT
NM_001128425.2:c.1000C>T
NM_001293190.2:c.961C>T
NM_001293191.2:c.949C>T
NM_001293192.2:c.640C>T
NM_001293195.2:c.916C>T
NM_001293196.2:c.640C>T
NM_001350650.2:c.571C>T
NM_001350651.2:c.571C>T
NM_012222.3:c.991C>T
NP_001041636.2:p.Pro306Ser
NP_001041637.1:p.Pro307Ser
NP_001041638.1:p.Pro306Ser
NP_001041639.1:p.Pro306Ser
NP_001121897.1:p.Pro334Ser
NP_001121897.1:p.Pro334Ser
NP_001280119.1:p.Pro321Ser
NP_001280120.1:p.Pro317Ser
NP_001280121.1:p.Pro214Ser
NP_001280124.1:p.Pro306Ser
NP_001280125.1:p.Pro214Ser
NP_001337579.1:p.Pro191Ser
NP_001337580.1:p.Pro191Ser
NP_036354.1:p.Pro331Ser
LRG_220t1:c.1000C>T
LRG_220:g.13624C>T
LRG_220p1:p.Pro334Ser
NC_000001.10:g.45797519G>A
NM_001128425.1:c.1000C>T
NR_146882.2:n.1144C>T
NR_146883.2:n.993C>T

Protein change:

P191S

Links:

dbSNP: rs587778537

NCBI 1000 Genomes Browser:

rs587778537

Molecular consequence:

NM_001048171.2:c.916C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001048172.2:c.919C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001048173.2:c.916C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001048174.2:c.916C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001128425.2:c.1000C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001293190.2:c.961C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001293191.2:c.949C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001293192.2:c.640C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001293195.2:c.916C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001293196.2:c.640C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350650.2:c.571C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350651.2:c.571C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_012222.3:c.991C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_146882.2:n.1144C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146883.2:n.993C>T - 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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USP21 ubiquitin specific peptidase 21 [Homo sapiens]
USP21 ubiquitin specific peptidase 21 [Homo sapiens]
Gene ID:27005

Gene
27005[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000961369	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 2, 2024)	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

SCV000961369

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 2, 2024)

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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000961369.6

#	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 proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 334 of the MUTYH protein (p.Pro334Ser). This variant is not present in population databases (gnomAD no frequency). 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: 662904). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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

Last Updated: Sep 29, 2024

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