NM_000535.7(PMS2):c.116del (p.Val39fs) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jun 21, 2024
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:: RCV000483540.3

Allele description [Variation Report for NM_000535.7(PMS2):c.116del (p.Val39fs)]

NM_000535.7(PMS2):c.116del (p.Val39fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.116del (p.Val39fs)

HGVS:

NC_000007.14:g.6005939del
NG_008466.1:g.8168del
NG_050738.1:g.1689del
NM_000535.5:c.116del
NM_000535.7:c.116delMANE SELECT
NM_001322003.2:c.-290del
NM_001322004.2:c.-242-1881del
NM_001322005.2:c.-290del
NM_001322006.2:c.116del
NM_001322007.2:c.-100del
NM_001322008.2:c.-52-1881del
NM_001322009.2:c.-290del
NM_001322010.2:c.-242-1881del
NM_001322011.2:c.-769del
NM_001322012.2:c.-769del
NM_001322013.2:c.-290del
NM_001322014.2:c.116del
NM_001322015.2:c.-369del
NP_000526.2:p.Val39fs
NP_001308935.1:p.Val39fs
NP_001308943.1:p.Val39fs
LRG_161t1:c.116del
LRG_161:g.8168del
NC_000007.13:g.6045570del
NM_000535.5:c.116delT
NM_000535.6:c.116del
NR_136154.1:n.203del

Protein change:

V39fs

Links:

dbSNP: rs1064794152

NCBI 1000 Genomes Browser:

rs1064794152

Molecular consequence:

NM_001322003.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-100del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-769del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-769del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-369del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.-242-1881del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1881del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1881del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.203del - 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
SCV000567993	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 21, 2024)	germline	clinical testing	Citation Link,
SCV001469600	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Dec 31, 2019)	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

SCV000567993

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 21, 2024)

germline

clinical testing

Citation Link,

SCV001469600

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Dec 31, 2019)

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
not provided	germline	yes	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, SCV000567993.4

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 21376568, 24362816)

#	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, SCV001469600.1

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

Description

The variant results in a shift of the reading frame, and is therefore predicted to result in the loss of a functional protein. Not found in the total gnomAD dataset, and the data is high quality.

#	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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