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NM_000535.7(PMS2):c.247_250dup (p.Thr84fs) AND Lynch syndrome 4

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 18, 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:
RCV003449209.1

Allele description [Variation Report for NM_000535.7(PMS2):c.247_250dup (p.Thr84fs)]

NM_000535.7(PMS2):c.247_250dup (p.Thr84fs)

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.247_250dup (p.Thr84fs)
HGVS:
  • NC_000007.14:g.6003972_6003975dup
  • NG_008466.1:g.10132_10135dup
  • NM_000535.7:c.247_250dupMANE SELECT
  • NM_001322003.2:c.-159_-156dup
  • NM_001322004.2:c.-159_-156dup
  • NM_001322005.2:c.-159_-156dup
  • NM_001322006.2:c.247_250dup
  • NM_001322007.2:c.32_35dup
  • NM_001322008.2:c.32_35dup
  • NM_001322009.2:c.-159_-156dup
  • NM_001322010.2:c.-159_-156dup
  • NM_001322011.2:c.-638_-635dup
  • NM_001322012.2:c.-638_-635dup
  • NM_001322013.2:c.-159_-156dup
  • NM_001322014.2:c.247_250dup
  • NM_001322015.2:c.-238_-235dup
  • NP_000526.2:p.Thr84fs
  • NP_001308935.1:p.Thr84fs
  • NP_001308936.1:p.Asn12_Asp13insTer
  • NP_001308937.1:p.Asn12_Asp13insTer
  • NP_001308943.1:p.Thr84fs
  • LRG_161t1:c.247_250dup
  • LRG_161:g.10132_10135dup
  • NC_000007.13:g.6043602_6043603insTTAA
  • NC_000007.13:g.6043603_6043606dup
  • NM_000535.5:c.247_250dupTTAA
  • NR_136154.1:n.334_337dup
Protein change:
T84fs
Links:
dbSNP: rs1554304940
NCBI 1000 Genomes Browser:
rs1554304940
Molecular consequence:
  • NM_001322003.2:c.-159_-156dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-159_-156dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-159_-156dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-159_-156dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322010.2:c.-159_-156dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-638_-635dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-638_-635dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-159_-156dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-238_-235dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000535.7:c.247_250dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322006.2:c.247_250dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322014.2:c.247_250dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322007.2:c.32_35dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322008.2:c.32_35dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NR_136154.1:n.334_337dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001322007.2:c.32_35dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322008.2:c.32_35dup - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004188690Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Pathogenic
(Sep 18, 2023) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV004188690.1

#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

Last Updated: Sep 29, 2024