NM_000535.7(PMS2):c.1121AGC[1] (p.Gln375del) AND PMS2-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 9, 2022
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:: RCV003413572.4

Allele description [Variation Report for NM_000535.7(PMS2):c.1121AGC[1] (p.Gln375del)]

NM_000535.7(PMS2):c.1121AGC[1] (p.Gln375del)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.1121AGC[1] (p.Gln375del)

HGVS:

NC_000007.14:g.5989819CTG[1]
NG_008466.1:g.24284AGC[1]
NM_000535.6:c.1124_1126delAGC
NM_000535.7:c.1121AGC[1]MANE SELECT
NM_001322003.2:c.716AGC[1]
NM_001322004.2:c.716AGC[1]
NM_001322005.2:c.716AGC[1]
NM_001322006.2:c.988+2153_988+2155del
NM_001322007.2:c.803AGC[1]
NM_001322008.2:c.803AGC[1]
NM_001322009.2:c.716AGC[1]
NM_001322010.2:c.583+2153_583+2155del
NM_001322011.2:c.188AGC[1]
NM_001322012.2:c.188AGC[1]
NM_001322013.2:c.548AGC[1]
NM_001322014.2:c.1121AGC[1]
NM_001322015.2:c.812AGC[1]
NP_000526.2:p.Gln375del
NP_001308932.1:p.Gln240del
NP_001308933.1:p.Gln240del
NP_001308934.1:p.Gln240del
NP_001308936.1:p.Gln269del
NP_001308937.1:p.Gln269del
NP_001308938.1:p.Gln240del
NP_001308940.1:p.Gln64del
NP_001308941.1:p.Gln64del
NP_001308942.1:p.Gln184del
NP_001308943.1:p.Gln375del
NP_001308944.1:p.Gln272del
LRG_161t1:c.1124_1126del
LRG_161:g.24284AGC[1]
NC_000007.13:g.6029449_6029451del
NC_000007.13:g.6029450CTG[1]
NM_000535.5:c.1124_1126del
NM_000535.5:c.1124_1126delAGC
NR_136154.1:n.1208AGC[1]

Protein change:

Q184del

Links:

dbSNP: rs1583334101

NCBI 1000 Genomes Browser:

rs1583334101

Molecular consequence:

NM_000535.7:c.1121AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322003.2:c.716AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322004.2:c.716AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322005.2:c.716AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322007.2:c.803AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322008.2:c.803AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322009.2:c.716AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322011.2:c.188AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322012.2:c.188AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322013.2:c.548AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322014.2:c.1121AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322015.2:c.812AGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322006.2:c.988+2153_988+2155del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2153_583+2155del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.1208AGC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: PMS2-related disorder
Synonyms:: PMS2-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004112971	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 9, 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

SCV004112971

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 9, 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	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 PreventionGenetics, part of Exact Sciences, SCV004112971.1

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

Description

The PMS2 c.1124_1126delAGC variant is predicted to result in an in-frame deletion (p.Gln375del). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. In ClinVar, this variant has been interpreted as uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/632949/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine