NM_000535.7(PMS2):c.632G>A (p.Arg211Gln) AND Lynch syndrome 4

Germline classification:: Uncertain significance (6 submissions)
Last evaluated:: Mar 19, 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:: RCV000412393.11

Allele description [Variation Report for NM_000535.7(PMS2):c.632G>A (p.Arg211Gln)]

NM_000535.7(PMS2):c.632G>A (p.Arg211Gln)

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.632G>A (p.Arg211Gln)

Other names:

p.R211Q:CGA>CAA

HGVS:

NC_000007.14:g.5999181C>T
NG_008466.1:g.14926G>A
NM_000535.7:c.632G>AMANE SELECT
NM_001322003.2:c.227G>A
NM_001322004.2:c.227G>A
NM_001322005.2:c.227G>A
NM_001322006.2:c.632G>A
NM_001322007.2:c.314G>A
NM_001322008.2:c.314G>A
NM_001322009.2:c.227G>A
NM_001322010.2:c.227G>A
NM_001322011.2:c.-302G>A
NM_001322012.2:c.-302G>A
NM_001322013.2:c.133-1758G>A
NM_001322014.2:c.632G>A
NM_001322015.2:c.323G>A
NP_000526.2:p.Arg211Gln
NP_001308932.1:p.Arg76Gln
NP_001308933.1:p.Arg76Gln
NP_001308934.1:p.Arg76Gln
NP_001308935.1:p.Arg211Gln
NP_001308936.1:p.Arg105Gln
NP_001308937.1:p.Arg105Gln
NP_001308938.1:p.Arg76Gln
NP_001308939.1:p.Arg76Gln
NP_001308943.1:p.Arg211Gln
NP_001308944.1:p.Arg108Gln
LRG_161t1:c.632G>A
LRG_161:g.14926G>A
NC_000007.13:g.6038812C>T
NM_000535.5:c.632G>A
NM_000535.6:c.632G>A
NR_136154.1:n.719G>A
p.R211Q

Protein change:

R105Q

Links:

dbSNP: rs587781934

NCBI 1000 Genomes Browser:

rs587781934

Molecular consequence:

NM_001322011.2:c.-302G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-302G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.133-1758G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.314G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.314G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.323G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.719G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Lynch syndrome 4 (LYNCH4)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:: MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000487980	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Dec 9, 2015)	unknown	clinical testing	Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV001440466	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 1, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001446382	University of Washington Department of Laboratory Medicine, University of Washington	no assertion criteria provided	Likely benign (Nov 1, 2019)	unknown	research
SCV004019788	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Uncertain significance (Apr 4, 2023)	unknown	clinical testing	Citation Link,
SCV004041796	Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	no assertion criteria provided	Uncertain significance (Oct 9, 2023)	germline	clinical testing
SCV005056392	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 19, 2024)	unknown	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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, research

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 Counsyl, SCV000487980.2

#	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 Institute of Human Genetics, University of Leipzig Medical Center, SCV001440466.1

#	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	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From University of Washington Department of Laboratory Medicine, University of Washington, SCV001446382.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV004019788.1

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

Description

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

#	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 Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004041796.1

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

From Baylor Genetics, SCV005056392.1

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

Last Updated: Oct 20, 2024

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