NM_000535.7(PMS2):c.164-9_178delinsGATCC AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 12, 2018
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:: RCV000985902.2

Allele description [Variation Report for NM_000535.7(PMS2):c.164-9_178delinsGATCC]

NM_000535.7(PMS2):c.164-9_178delinsGATCC

Gene:

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

Variant type:

Indel

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.164-9_178delinsGATCC

HGVS:

NC_000007.14:g.6004044_6004067del24insGGATC
NC_000007.14:g.6004044_6004067delinsGGATC
NG_008466.1:g.10040_10063delinsGATCC
NM_000535.7:c.164-9_178delinsGATCCMANE SELECT
NM_001322003.2:c.-242-9_-228delinsGATCC
NM_001322004.2:c.-242-9_-228delinsGATCC
NM_001322005.2:c.-242-9_-228delinsGATCC
NM_001322006.2:c.164-9_178delinsGATCC
NM_001322007.2:c.-52-9_-38delinsGATCC
NM_001322008.2:c.-52-9_-38delinsGATCC
NM_001322009.2:c.-242-9_-228delinsGATCC
NM_001322010.2:c.-242-9_-228delinsGATCC
NM_001322011.2:c.-721-9_-707delinsGATCC
NM_001322012.2:c.-721-9_-707delinsGATCC
NM_001322013.2:c.-242-9_-228delinsGATCC
NM_001322014.2:c.164-9_178delinsGATCC
NM_001322015.2:c.-321-9_-307delinsGATCC
LRG_161t1:c.164-9_178del24insGATCC
LRG_161:g.10040_10063delinsGATCC
NC_000007.13:g.6043675_6043698delinsGGATC
NM_000535.5:c.164-9_178del24insGATCC
NM_000535.6:c.164-9_178delinsGATCC

Links:

dbSNP: rs1583410952

NCBI 1000 Genomes Browser:

rs1583410952

Molecular consequence:

NM_000535.7:c.164-9_178delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322003.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322004.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322005.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322006.2:c.164-9_178delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322007.2:c.-52-9_-38delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322008.2:c.-52-9_-38delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322009.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322010.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322011.2:c.-721-9_-707delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322012.2:c.-721-9_-707delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322013.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322014.2:c.164-9_178delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322015.2:c.-321-9_-307delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001134583	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Dec 12, 2018)	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

SCV001134583

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Dec 12, 2018)

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

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, SCV001134583.2

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

Description

The variant may result in the deletion of at least one complete exon, 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 (0/279944 chr).

#	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: Aug 11, 2024

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