NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 4, 2022
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:: RCV000413126.5

Allele description [Variation Report for NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter)]

NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter)

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.2404C>T (p.Arg802Ter)

HGVS:

NC_000007.14:g.5977629G>A
NG_008466.1:g.36478C>T
NM_000535.7:c.2404C>TMANE SELECT
NM_001322003.2:c.1999C>T
NM_001322004.2:c.1999C>T
NM_001322005.2:c.1999C>T
NM_001322006.2:c.2248C>T
NM_001322007.2:c.2086C>T
NM_001322008.2:c.2086C>T
NM_001322009.2:c.2032C>T
NM_001322010.2:c.1843C>T
NM_001322011.2:c.1471C>T
NM_001322012.2:c.1471C>T
NM_001322013.2:c.1831C>T
NM_001322014.2:c.2437C>T
NM_001322015.2:c.2095C>T
NP_000526.2:p.Arg802Ter
NP_001308932.1:p.Arg667Ter
NP_001308933.1:p.Arg667Ter
NP_001308934.1:p.Arg667Ter
NP_001308935.1:p.Arg750Ter
NP_001308936.1:p.Arg696Ter
NP_001308937.1:p.Arg696Ter
NP_001308938.1:p.Arg678Ter
NP_001308939.1:p.Arg615Ter
NP_001308940.1:p.Arg491Ter
NP_001308941.1:p.Arg491Ter
NP_001308942.1:p.Arg611Ter
NP_001308943.1:p.Arg813Ter
NP_001308944.1:p.Arg699Ter
LRG_161t1:c.2404C>T
LRG_161:g.36478C>T
NC_000007.13:g.6017260G>A
NM_000535.5:c.2404C>T
NM_000535.6:c.2404C>T
NR_136154.1:n.2448C>T
p.R802*

Protein change:

R491*; ARG802TER

Links:

OMIM: 600259.0004; dbSNP: rs63751466

NCBI 1000 Genomes Browser:

rs63751466

Molecular consequence:

NR_136154.1:n.2448C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.2404C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322003.2:c.1999C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322004.2:c.1999C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322005.2:c.1999C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322006.2:c.2248C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322007.2:c.2086C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322008.2:c.2086C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322009.2:c.2032C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322010.2:c.1843C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322011.2:c.1471C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322012.2:c.1471C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322013.2:c.1831C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322014.2:c.2437C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322015.2:c.2095C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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NOL1/NOP2/sun family protein / antitermination NusB domain-containing protein [A...
NOL1/NOP2/sun family protein / antitermination NusB domain-containing protein [Arabidopsis thaliana]
gi|22331043|ref|NP_187924.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000490734	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 4, 2022)	germline	clinical testing	Citation Link,
SCV005197199	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 27, 2022)	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

SCV000490734

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 4, 2022)

germline

clinical testing

Citation Link,

SCV005197199

Clinical Genetics Laboratory, Skane University Hospital Lund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 27, 2022)

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	yes	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 GeneDx, SCV000490734.4

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

Description

Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 61 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (HGMD); Observed in the heterozygous state in individuals with Lynch syndrome-related tumors (Senter et al., 2008; Vaughn et al., 2010; Ten Broeke et al., 2015; Rosty et al., 2016; Andrianova et al., 2017; Manchana et al., 2021); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 15077197, 18602922, 18709565, 15340263, 17993636, 25512458, 25525159, 25691505, 17851451, 21376568, 20205264, 21356188, 28514183, 28152038, 26895986, 28805995, 32876971, 32029870, 31433215, 32773772, 30787465, 18619468, Fukui2011[Chapter], 34048176, 33372952, 16507833)

#	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 Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005197199.1

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

Last Updated: Oct 8, 2024

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