NM_000535.7(PMS2):c.1970del (p.Asn657fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 20, 2020
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:: RCV001284204.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1970del (p.Asn657fs)]

NM_000535.7(PMS2):c.1970del (p.Asn657fs)

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.1970del (p.Asn657fs)

HGVS:

NC_000007.14:g.5986798del
NG_008466.1:g.27312del
NM_000535.7:c.1970delMANE SELECT
NM_001322003.2:c.1565del
NM_001322004.2:c.1565del
NM_001322005.2:c.1565del
NM_001322006.2:c.1814del
NM_001322007.2:c.1652del
NM_001322008.2:c.1652del
NM_001322009.2:c.1565del
NM_001322010.2:c.1409del
NM_001322011.2:c.1037del
NM_001322012.2:c.1037del
NM_001322013.2:c.1397del
NM_001322014.2:c.1970del
NM_001322015.2:c.1661del
NP_000526.2:p.Asn657fs
NP_001308932.1:p.Asn522fs
NP_001308933.1:p.Asn522fs
NP_001308934.1:p.Asn522fs
NP_001308935.1:p.Asn605fs
NP_001308936.1:p.Asn551fs
NP_001308937.1:p.Asn551fs
NP_001308938.1:p.Asn522fs
NP_001308939.1:p.Asn470fs
NP_001308940.1:p.Asn346fs
NP_001308941.1:p.Asn346fs
NP_001308942.1:p.Asn466fs
NP_001308943.1:p.Asn657fs
NP_001308944.1:p.Asn554fs
LRG_161t1:c.1970del
LRG_161:g.27312del
NC_000007.13:g.6026426del
NC_000007.13:g.6026429del
NM_000535.5:c.1970del
NM_000535.5:c.1970delA
NM_000535.6:c.1970del
NR_136154.1:n.2057del

Protein change:

N346fs

Links:

dbSNP: rs1064794566

NCBI 1000 Genomes Browser:

rs1064794566

Molecular consequence:

NM_000535.7:c.1970del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.1814del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.1652del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.1652del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1409del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.1037del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.1037del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1397del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.1970del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.1661del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2057del - 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
SCV001469861	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Jul 20, 2020)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24689082, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001469861

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Jul 20, 2020)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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 massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes.

Hansen MF, Neckmann U, Lavik LA, Vold T, Gilde B, Toft RK, Sjursen W.

Mol Genet Genomic Med. 2014 Mar;2(2):186-200. doi: 10.1002/mgg3.62. Epub 2014 Jan 21.

PubMed [citation]

PMID:: 24689082
PMCID:: PMC3960061

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, SCV001469861.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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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