NM_000535.7(PMS2):c.2062A>G (p.Ile688Val) AND Lynch syndrome 4

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 3, 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:: RCV000662654.3

Allele description [Variation Report for NM_000535.7(PMS2):c.2062A>G (p.Ile688Val)]

NM_000535.7(PMS2):c.2062A>G (p.Ile688Val)

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.2062A>G (p.Ile688Val)

HGVS:

NC_000007.14:g.5982936T>C
NG_008466.1:g.31171A>G
NM_000535.7:c.2062A>GMANE SELECT
NM_001322003.2:c.1657A>G
NM_001322004.2:c.1657A>G
NM_001322005.2:c.1657A>G
NM_001322006.2:c.1906A>G
NM_001322007.2:c.1744A>G
NM_001322008.2:c.1744A>G
NM_001322009.2:c.1657A>G
NM_001322010.2:c.1501A>G
NM_001322011.2:c.1129A>G
NM_001322012.2:c.1129A>G
NM_001322013.2:c.1489A>G
NM_001322014.2:c.2062A>G
NM_001322015.2:c.1753A>G
NP_000526.2:p.Ile688Val
NP_001308932.1:p.Ile553Val
NP_001308933.1:p.Ile553Val
NP_001308934.1:p.Ile553Val
NP_001308935.1:p.Ile636Val
NP_001308936.1:p.Ile582Val
NP_001308937.1:p.Ile582Val
NP_001308938.1:p.Ile553Val
NP_001308939.1:p.Ile501Val
NP_001308940.1:p.Ile377Val
NP_001308941.1:p.Ile377Val
NP_001308942.1:p.Ile497Val
NP_001308943.1:p.Ile688Val
NP_001308944.1:p.Ile585Val
LRG_161t1:c.2062A>G
LRG_161:g.31171A>G
NC_000007.13:g.6022567T>C
NM_000535.5:c.2062A>G
NM_000535.6:c.2062A>G
NR_136154.1:n.2149A>G

Protein change:

I377V

Links:

dbSNP: rs1060503144

NCBI 1000 Genomes Browser:

rs1060503144

Molecular consequence:

NM_000535.7:c.2062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1906A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1744A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1744A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.1501A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.1129A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.1129A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1489A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.2062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1753A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.2149A>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000785341	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Jul 7, 2017)	unknown	clinical testing	Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf, Citation Link,
SCV001137283	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Uncertain significance (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV004019752	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Uncertain significance (Apr 3, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000785341

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(Jul 7, 2017)

unknown

clinical testing

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf,

Citation Link,

SCV001137283

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Uncertain significance
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV004019752

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Uncertain significance
(Apr 3, 2023)

unknown

clinical testing

Citation Link

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

Details of each submission

From Counsyl, SCV000785341.2

#	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 Mendelics, SCV001137283.1

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

From Myriad Genetics, Inc., SCV004019752.1

#	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

Last Updated: Sep 29, 2024

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