NM_000535.7(PMS2):c.1119T>A (p.Ser373Arg) AND Lynch syndrome 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 8, 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:: RCV003459493.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1119T>A (p.Ser373Arg)]

NM_000535.7(PMS2):c.1119T>A (p.Ser373Arg)

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.1119T>A (p.Ser373Arg)

HGVS:

NC_000007.14:g.5989825A>T
NG_008466.1:g.24282T>A
NM_000535.7:c.1119T>AMANE SELECT
NM_001322003.2:c.714T>A
NM_001322004.2:c.714T>A
NM_001322005.2:c.714T>A
NM_001322006.2:c.988+2148T>A
NM_001322007.2:c.801T>A
NM_001322008.2:c.801T>A
NM_001322009.2:c.714T>A
NM_001322010.2:c.583+2148T>A
NM_001322011.2:c.186T>A
NM_001322012.2:c.186T>A
NM_001322013.2:c.546T>A
NM_001322014.2:c.1119T>A
NM_001322015.2:c.810T>A
NP_000526.2:p.Ser373Arg
NP_001308932.1:p.Ser238Arg
NP_001308933.1:p.Ser238Arg
NP_001308934.1:p.Ser238Arg
NP_001308936.1:p.Ser267Arg
NP_001308937.1:p.Ser267Arg
NP_001308938.1:p.Ser238Arg
NP_001308940.1:p.Ser62Arg
NP_001308941.1:p.Ser62Arg
NP_001308942.1:p.Ser182Arg
NP_001308943.1:p.Ser373Arg
NP_001308944.1:p.Ser270Arg
LRG_161t1:c.1119T>A
LRG_161:g.24282T>A
NC_000007.13:g.6029456A>T
NM_000535.5:c.1119T>A
NR_136154.1:n.1206T>A

Protein change:

S182R

Links:

dbSNP: rs1060503147

NCBI 1000 Genomes Browser:

rs1060503147

Molecular consequence:

NM_001322006.2:c.988+2148T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2148T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.1119T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.714T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.714T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.714T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.801T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.801T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.714T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.186T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.186T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.546T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1119T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.1206T>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
SCV004205490	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 8, 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

SCV004205490

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 8, 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 Baylor Genetics, SCV004205490.1

#	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: Sep 29, 2024

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