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NM_000535.7(PMS2):c.512del (p.Lys171fs) AND Lynch syndrome 4

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 19, 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:
RCV003454164.1

Allele description [Variation Report for NM_000535.7(PMS2):c.512del (p.Lys171fs)]

NM_000535.7(PMS2):c.512del (p.Lys171fs)

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.512del (p.Lys171fs)
HGVS:
  • NC_000007.14:g.6002479del
  • NG_008466.1:g.11629del
  • NM_000535.7:c.512delMANE SELECT
  • NM_001018040.1:c.106delA
  • NM_001322003.2:c.107del
  • NM_001322004.2:c.107del
  • NM_001322005.2:c.107del
  • NM_001322006.2:c.512del
  • NM_001322007.2:c.194del
  • NM_001322008.2:c.194del
  • NM_001322009.2:c.107del
  • NM_001322010.2:c.107del
  • NM_001322011.2:c.-373del
  • NM_001322012.2:c.-373del
  • NM_001322013.2:c.107del
  • NM_001322014.2:c.512del
  • NM_001322015.2:c.203del
  • NM_001406866.1:c.697delA
  • NM_001406868.1:c.535delA
  • NM_001406869.1:c.511delA
  • NM_001406870.1:c.511delA
  • NM_001406871.1:c.511delA
  • NM_001406872.1:c.511delA
  • NM_001406873.1:c.511delA
  • NM_001406874.1:c.511delA
  • NM_001406875.1:c.202delA
  • NM_001406876.1:c.193delA
  • NM_001406877.1:c.202delA
  • NM_001406878.1:c.202delA
  • NM_001406879.1:c.202delA
  • NM_001406880.1:c.202delA
  • NM_001406881.1:c.202delA
  • NM_001406882.1:c.202delA
  • NM_001406883.1:c.193delA
  • NM_001406884.1:c.511delA
  • NM_001406886.1:c.511delA
  • NM_001406887.1:c.106delA
  • NM_001406888.1:c.106delA
  • NM_001406889.1:c.106delA
  • NM_001406890.1:c.106delA
  • NM_001406891.1:c.106delA
  • NM_001406892.1:c.106delA
  • NM_001406893.1:c.106delA
  • NM_001406894.1:c.106delA
  • NM_001406895.1:c.106delA
  • NM_001406896.1:c.106delA
  • NM_001406897.1:c.106delA
  • NM_001406898.1:c.106delA
  • NM_001406899.1:c.106delA
  • NM_001406900.1:c.202delA
  • NM_001406901.1:c.193delA
  • NM_001406902.1:c.193delA
  • NM_001406903.1:c.193delA
  • NM_001406904.1:c.106delA
  • NM_001406905.1:c.106delA
  • NM_001406906.1:c.106delA
  • NM_001406907.1:c.106delA
  • NM_001406908.1:c.106delA
  • NM_001406909.1:c.106delA
  • NM_001406910.1:c.106delA
  • NM_001406911.1:c.106delA
  • NM_001406912.1:c.511delA
  • NP_000526.1:p.Lys171Argfs
  • NP_000526.2:p.Lys171fs
  • NP_001018050.1:p.Lys36Argfs
  • NP_001308932.1:p.Lys36fs
  • NP_001308933.1:p.Lys36fs
  • NP_001308934.1:p.Lys36fs
  • NP_001308935.1:p.Lys171fs
  • NP_001308936.1:p.Lys65fs
  • NP_001308937.1:p.Lys65fs
  • NP_001308938.1:p.Lys36fs
  • NP_001308939.1:p.Lys36fs
  • NP_001308942.1:p.Lys36fs
  • NP_001308943.1:p.Lys171fs
  • NP_001308944.1:p.Lys68fs
  • NP_001393795.1:p.Lys233Argfs
  • NP_001393797.1:p.Lys179Argfs
  • NP_001393798.1:p.Lys171Argfs
  • NP_001393799.1:p.Lys171Argfs
  • NP_001393800.1:p.Lys171Argfs
  • NP_001393801.1:p.Lys171Argfs
  • NP_001393802.1:p.Lys171Argfs
  • NP_001393803.1:p.Lys171Argfs
  • NP_001393804.1:p.Lys68Argfs
  • NP_001393805.1:p.Lys65Argfs
  • NP_001393806.1:p.Lys68Argfs
  • NP_001393807.1:p.Lys68Argfs
  • NP_001393808.1:p.Lys68Argfs
  • NP_001393809.1:p.Lys68Argfs
  • NP_001393810.1:p.Lys68Argfs
  • NP_001393811.1:p.Lys68Argfs
  • NP_001393812.1:p.Lys65Argfs
  • NP_001393813.1:p.Lys171Argfs
  • NP_001393815.1:p.Lys171Argfs
  • NP_001393816.1:p.Lys36Argfs
  • NP_001393817.1:p.Lys36Argfs
  • NP_001393818.1:p.Lys36Argfs
  • NP_001393819.1:p.Lys36Argfs
  • NP_001393820.1:p.Lys36Argfs
  • NP_001393821.1:p.Lys36Argfs
  • NP_001393822.1:p.Lys36Argfs
  • NP_001393823.1:p.Lys36Argfs
  • NP_001393824.1:p.Lys36Argfs
  • NP_001393825.1:p.Lys36Argfs
  • NP_001393826.1:p.Lys36Argfs
  • NP_001393827.1:p.Lys36Argfs
  • NP_001393828.1:p.Lys36Argfs
  • NP_001393829.1:p.Lys68Argfs
  • NP_001393830.1:p.Lys65Argfs
  • NP_001393831.1:p.Lys65Argfs
  • NP_001393832.1:p.Lys65Argfs
  • NP_001393833.1:p.Lys36Argfs
  • NP_001393834.1:p.Lys36Argfs
  • NP_001393835.1:p.Lys36Argfs
  • NP_001393836.1:p.Lys36Argfs
  • NP_001393837.1:p.Lys36Argfs
  • NP_001393838.1:p.Lys36Argfs
  • NP_001393839.1:p.Lys36Argfs
  • NP_001393840.1:p.Lys36Argfs
  • NP_001393841.1:p.Lys171Argfs
  • LRG_161t1:c.511del
  • LRG_161:g.11629del
  • LRG_161p1:p.Lys171Argfs
  • NC_000007.13:g.6042110del
  • NM_000535.5:c.511delA
  • NM_000535.5:c.512delA
  • NR_003085.2:n.593delA
  • NR_136154.1:n.599del
Protein change:
K171fs
Molecular consequence:
  • NM_001322011.2:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000535.7:c.512del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001018040.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322003.2:c.107del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322004.2:c.107del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322005.2:c.107del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322006.2:c.512del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322007.2:c.194del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322008.2:c.194del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322009.2:c.107del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322010.2:c.107del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322013.2:c.107del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322014.2:c.512del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322015.2:c.203del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406866.1:c.697delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406868.1:c.535delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406869.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406870.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406871.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406872.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406873.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406874.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406875.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406876.1:c.193delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406877.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406878.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406879.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406880.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406881.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406882.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406883.1:c.193delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406884.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406886.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406887.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406888.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406889.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406890.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406891.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406892.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406893.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406894.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406895.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406896.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406897.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406898.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406899.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406900.1:c.202delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406901.1:c.193delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406902.1:c.193delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406903.1:c.193delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406904.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406905.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406906.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406907.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406908.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406909.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406910.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406911.1:c.106delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406912.1:c.511delA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_136154.1:n.599del - 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004187699Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Pathogenic
(Sep 19, 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., SCV004187699.1

#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: May 1, 2024