NM_000535.7(PMS2):c.125TAG[1] (p.Val43del) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 14, 2020
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:: RCV000485398.2

Allele description [Variation Report for NM_000535.7(PMS2):c.125TAG[1] (p.Val43del)]

NM_000535.7(PMS2):c.125TAG[1] (p.Val43del)

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.125TAG[1] (p.Val43del)

HGVS:

NC_000007.14:g.6005925CTA[1]
NG_008466.1:g.8177TAG[1]
NG_050738.1:g.1675CTA[1]
NM_000535.7:c.125TAG[1]MANE SELECT
NM_001322003.2:c.-281TAG[1]
NM_001322004.2:c.-242-1869_-242-1867del
NM_001322005.2:c.-281TAG[1]
NM_001322006.2:c.125TAG[1]
NM_001322007.2:c.-91TAG[1]
NM_001322008.2:c.-52-1869_-52-1867del
NM_001322009.2:c.-281TAG[1]
NM_001322010.2:c.-242-1869_-242-1867del
NM_001322011.2:c.-760TAG[1]
NM_001322012.2:c.-760TAG[1]
NM_001322013.2:c.-281TAG[1]
NM_001322014.2:c.125TAG[1]
NM_001322015.2:c.-360TAG[1]
NP_000526.2:p.Val43del
NP_001308935.1:p.Val43del
NP_001308943.1:p.Val43del
LRG_161t1:c.128_130del
LRG_161:g.8177TAG[1]
NC_000007.13:g.6045556CTA[1]
NC_000007.13:g.6045556_6045558del
NM_000535.5:c.128_130delTAG
NM_000535.6:c.128_130del
NR_136154.1:n.212TAG[1]

Protein change:

V43del

Links:

dbSNP: rs1064794820

NCBI 1000 Genomes Browser:

rs1064794820

Molecular consequence:

NM_001322003.2:c.-281TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-281TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-91TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-281TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-760TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-760TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-281TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-360TAG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.125TAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322006.2:c.125TAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322014.2:c.125TAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001322004.2:c.-242-1869_-242-1867del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1869_-52-1867del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1869_-242-1867del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.212TAG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000570006	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Apr 19, 2016)	germline	clinical testing	Citation Link,
SCV001469604	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Aug 14, 2020)	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

SCV000570006

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Apr 19, 2016)

germline

clinical testing

Citation Link,

SCV001469604

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Aug 14, 2020)

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	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000570006.4

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

Description

This in-frame deletion of 3 nucleotides in PMS2 is denoted c.128_130delTAG at the cDNA level and p.Val43del (V43del) at the protein level. The normal sequence, with the bases that are deleted in braces, is TTAG[TAG]AAAAC. This deletion of a single Valine residue occurs at a position where amino acids with properties similar to Valine are tolerated across species and is located within the ATPase domain (Guarne 2001, Fukui 2011). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. Since in-frame deletions may or may not inhibit proper protein functioning, the clinical significance of this finding remains unclear at this time, and we consider PMS2 Val43del to be a variant of uncertain significance.

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001469604.1

#	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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