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NM_000535.7(PMS2):c.1970del (p.Asn657fs) AND Lynch syndrome 4

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Sep 21, 2023
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:
RCV003451333.2

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)

Name:
Lynch syndrome 4 (LYNCH4)
Synonyms:
Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:
MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004187666Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Pathogenic
(Sep 21, 2023) 		unknownclinical testing

Citation Link,

SCV004203423Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 27, 2021) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Myriad Genetics, Inc., SCV004187666.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004203423.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024