NM_000535.7(PMS2):c.353+3G>A AND Lynch syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 15, 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:: RCV004000433.2

Allele description [Variation Report for NM_000535.7(PMS2):c.353+3G>A]

NM_000535.7(PMS2):c.353+3G>A

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.353+3G>A

HGVS:

NC_000007.14:g.6003687C>T
NG_008466.1:g.10420G>A
NM_000535.7:c.353+3G>AMANE SELECT
NM_001322003.2:c.-53+3G>A
NM_001322004.2:c.-53+3G>A
NM_001322005.2:c.-53+3G>A
NM_001322006.2:c.353+3G>A
NM_001322007.2:c.35+285G>A
NM_001322008.2:c.35+285G>A
NM_001322009.2:c.-53+3G>A
NM_001322010.2:c.-53+3G>A
NM_001322011.2:c.-532+3G>A
NM_001322012.2:c.-532+3G>A
NM_001322013.2:c.-53+3G>A
NM_001322014.2:c.353+3G>A
NM_001322015.2:c.-132+3G>A
LRG_161t1:c.353+3G>A
LRG_161:g.10420G>A
NC_000007.13:g.6043318C>T
NM_000535.5:c.353+3G>A

Links:

dbSNP: rs766373982

NCBI 1000 Genomes Browser:

rs766373982

Molecular consequence:

NM_000535.7:c.353+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.353+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.35+285G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+285G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-532+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-532+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.353+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.-132+3G>A - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Lynch syndrome
Identifiers:: MONDO: MONDO:0005835; MedGen: C4552100

Recent activity

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alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A [Misgurn...
alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A [Misgurnus anguillicaudatus]
gi|2489393405|ref|XP_055074447.1|

Protein
PREDICTED: Homo sapiens sacsin molecular chaperone (SACS), transcript variant X1...
PREDICTED: Homo sapiens sacsin molecular chaperone (SACS), transcript variant X11, mRNA
gi|2217294120|ref|XM_047430260.1|

Nucleotide
Gm23557 predicted gene, 23557 [Mus musculus]
Gm23557 predicted gene, 23557 [Mus musculus]
Gene ID:115489217

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004826363	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Aug 15, 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

SCV004826363

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Aug 15, 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	unknown	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

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 All of Us Research Program, National Institutes of Health, SCV004826363.1

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

Description

This variant causes a G to A nucleotide substitution at the +3 position of intron 4 of the PMS2 gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with PMS2-related disorders in the literature. This variant has been identified in 1/234666 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is 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	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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