NM_000535.7(PMS2):c.89A>G (p.Gln30Arg) AND Lynch syndrome 4

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Nov 29, 2023
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:: RCV000410641.5

Allele description [Variation Report for NM_000535.7(PMS2):c.89A>G (p.Gln30Arg)]

NM_000535.7(PMS2):c.89A>G (p.Gln30Arg)

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.89A>G (p.Gln30Arg)

HGVS:

NC_000007.14:g.6005966T>C
NG_008466.1:g.8141A>G
NG_050738.1:g.1716T>C
NM_000535.7:c.89A>GMANE SELECT
NM_001322003.2:c.-317A>G
NM_001322004.2:c.-242-1908A>G
NM_001322005.2:c.-317A>G
NM_001322006.2:c.89A>G
NM_001322007.2:c.-127A>G
NM_001322008.2:c.-52-1908A>G
NM_001322009.2:c.-317A>G
NM_001322010.2:c.-242-1908A>G
NM_001322011.2:c.-796A>G
NM_001322012.2:c.-796A>G
NM_001322013.2:c.-317A>G
NM_001322014.2:c.89A>G
NM_001322015.2:c.-396A>G
NP_000526.2:p.Gln30Arg
NP_001308935.1:p.Gln30Arg
NP_001308943.1:p.Gln30Arg
LRG_161t1:c.89A>G
LRG_161:g.8141A>G
NC_000007.13:g.6045597T>C
NM_000535.5:c.89A>G
NM_000535.6:c.89A>G
NR_136154.1:n.176A>G
p.Q30R

Protein change:

Q30R

Links:

dbSNP: rs56203955

NCBI 1000 Genomes Browser:

rs56203955

Molecular consequence:

NM_001322003.2:c.-317A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-317A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-127A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-317A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-796A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-796A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-317A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-396A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1908A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1908A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1908A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.89A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.89A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.89A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.176A>G - 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

Recent activity

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fbp [Escherichia coli O157:H7 str. Sakai]
Gene ID:913877

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000489607	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Oct 26, 2016)	unknown	clinical testing	Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV004019849	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,
SCV004207859	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 29, 2023)	unknown	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

SCV000489607

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(Oct 26, 2016)

unknown

clinical testing

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV004019849

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,

SCV004207859

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 29, 2023)

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

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, SCV000489607.2

#	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 Myriad Genetics, Inc., SCV004019849.1

#	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 Baylor Genetics, SCV004207859.2

#	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: Sep 29, 2024

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