NM_000535.7(PMS2):c.1924del (p.Glu642fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 4, 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:: RCV003478895.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1924del (p.Glu642fs)]

NM_000535.7(PMS2):c.1924del (p.Glu642fs)

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.1924del (p.Glu642fs)

HGVS:

NC_000007.14:g.5986844del
NG_008466.1:g.27266del
NM_000535.6:c.1924del
NM_000535.7:c.1924delMANE SELECT
NM_001322003.2:c.1519del
NM_001322004.2:c.1519del
NM_001322005.2:c.1519del
NM_001322006.2:c.1768del
NM_001322007.2:c.1606del
NM_001322008.2:c.1606del
NM_001322009.2:c.1519del
NM_001322010.2:c.1363del
NM_001322011.2:c.991del
NM_001322012.2:c.991del
NM_001322013.2:c.1351del
NM_001322014.2:c.1924del
NM_001322015.2:c.1615del
NP_000526.2:p.Glu642fs
NP_001308932.1:p.Glu507fs
NP_001308933.1:p.Glu507fs
NP_001308934.1:p.Glu507fs
NP_001308935.1:p.Glu590fs
NP_001308936.1:p.Glu536fs
NP_001308937.1:p.Glu536fs
NP_001308938.1:p.Glu507fs
NP_001308939.1:p.Glu455fs
NP_001308940.1:p.Glu331fs
NP_001308941.1:p.Glu331fs
NP_001308942.1:p.Glu451fs
NP_001308943.1:p.Glu642fs
NP_001308944.1:p.Glu539fs
LRG_161:g.27266del
NC_000007.13:g.6026472del
NC_000007.13:g.6026475del
NR_136154.1:n.2011del

Protein change:

E331fs

Links:

dbSNP: rs2128721171

NCBI 1000 Genomes Browser:

rs2128721171

Molecular consequence:

NM_000535.7:c.1924del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.1519del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.1519del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.1519del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.1768del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.1606del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.1606del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.1519del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1363del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.991del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.991del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.1924del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.1615del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2011del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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NADH dehydrogenase subunit 4L (mitochondrion) [Marsupiomonas sp. NIES 1824]
NADH dehydrogenase subunit 4L (mitochondrion) [Marsupiomonas sp. NIES 1824]
gi|1829529729|gb|QIV68126.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004218967	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (May 4, 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

SCV004218967

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(May 4, 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

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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004218967.1

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

Description

This frameshift variant alters the translational reading frame of the PMS2 mRNA and is predicted to cause the premature termination of PMS2 protein synthesis. The variant has not been reported in individuals with PMS2-related diseases in the published literature. It also has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as likely pathogenic.

#	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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