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NM_000535.7(PMS2):c.1415_1418del (p.Lys472fs) AND Lynch syndrome 4

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 9, 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:
RCV003450581.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1415_1418del (p.Lys472fs)]

NM_000535.7(PMS2):c.1415_1418del (p.Lys472fs)

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.1415_1418del (p.Lys472fs)
HGVS:
  • NC_000007.14:g.5987350_5987353del
  • NG_008466.1:g.26757_26760del
  • NM_000535.7:c.1415_1418delMANE SELECT
  • NM_001018040.1:c.1007_1010delAGAA
  • NM_001322003.2:c.1010_1013del
  • NM_001322004.2:c.1010_1013del
  • NM_001322005.2:c.1010_1013del
  • NM_001322006.2:c.1259_1262del
  • NM_001322007.2:c.1097_1100del
  • NM_001322008.2:c.1097_1100del
  • NM_001322009.2:c.1010_1013del
  • NM_001322010.2:c.854_857del
  • NM_001322011.2:c.482_485del
  • NM_001322012.2:c.482_485del
  • NM_001322013.2:c.842_845del
  • NM_001322014.2:c.1415_1418del
  • NM_001322015.2:c.1106_1109del
  • NM_001406866.1:c.1601_1604del
  • NM_001406868.1:c.1439_1442del
  • NM_001406869.1:c.1307_1310del
  • NM_001406870.1:c.1259_1262del
  • NM_001406871.1:c.1415_1418del
  • NM_001406872.1:c.1415_1418del
  • NM_001406873.1:c.1217_1220del
  • NM_001406874.1:c.1247_1250del
  • NM_001406875.1:c.1106_1109del
  • NM_001406876.1:c.1097_1100del
  • NM_001406877.1:c.1106_1109del
  • NM_001406878.1:c.1106_1109del
  • NM_001406879.1:c.1106_1109del
  • NM_001406880.1:c.1106_1109del
  • NM_001406881.1:c.1106_1109del
  • NM_001406882.1:c.1106_1109del
  • NM_001406883.1:c.1097_1100del
  • NM_001406884.1:c.1091_1094del
  • NM_001406885.1:c.1079_1082del
  • NM_001406886.1:c.1049_1052del
  • NM_001406887.1:c.1010_1013del
  • NM_001406888.1:c.1010_1013del
  • NM_001406889.1:c.1010_1013del
  • NM_001406890.1:c.1010_1013del
  • NM_001406891.1:c.1010_1013del
  • NM_001406892.1:c.1010_1013del
  • NM_001406893.1:c.1010_1013del
  • NM_001406894.1:c.1010_1013del
  • NM_001406895.1:c.1010_1013del
  • NM_001406896.1:c.1010_1013del
  • NM_001406897.1:c.1010_1013del
  • NM_001406898.1:c.1010_1013del
  • NM_001406899.1:c.1010_1013del
  • NM_001406900.1:c.950_953del
  • NM_001406901.1:c.941_944del
  • NM_001406902.1:c.941_944del
  • NM_001406903.1:c.1097_1100del
  • NM_001406904.1:c.902_905del
  • NM_001406905.1:c.902_905del
  • NM_001406906.1:c.854_857del
  • NM_001406907.1:c.854_857del
  • NM_001406908.1:c.1010_1013del
  • NM_001406909.1:c.842_845del
  • NM_001406910.1:c.1010_1013del
  • NM_001406911.1:c.644_647del
  • NM_001406912.1:c.804-4359_804-4356del
  • NP_000526.1:p.Lys472Argfs
  • NP_000526.2:p.Lys472fs
  • NP_001018050.1:p.Lys337Argfs
  • NP_001308932.1:p.Lys337fs
  • NP_001308933.1:p.Lys337fs
  • NP_001308934.1:p.Lys337fs
  • NP_001308935.1:p.Lys420fs
  • NP_001308936.1:p.Lys366fs
  • NP_001308937.1:p.Lys366fs
  • NP_001308938.1:p.Lys337fs
  • NP_001308939.1:p.Lys285fs
  • NP_001308940.1:p.Lys161fs
  • NP_001308941.1:p.Lys161fs
  • NP_001308942.1:p.Lys281fs
  • NP_001308943.1:p.Lys472fs
  • NP_001308944.1:p.Lys369fs
  • NP_001393795.1:p.Lys534fs
  • NP_001393797.1:p.Lys480fs
  • NP_001393798.1:p.Lys436fs
  • NP_001393799.1:p.Lys420fs
  • NP_001393800.1:p.Lys472fs
  • NP_001393801.1:p.Lys472fs
  • NP_001393802.1:p.Lys406fs
  • NP_001393803.1:p.Lys416fs
  • NP_001393804.1:p.Lys369fs
  • NP_001393805.1:p.Lys366fs
  • NP_001393806.1:p.Lys369fs
  • NP_001393807.1:p.Lys369fs
  • NP_001393808.1:p.Lys369fs
  • NP_001393809.1:p.Lys369fs
  • NP_001393810.1:p.Lys369fs
  • NP_001393811.1:p.Lys369fs
  • NP_001393812.1:p.Lys366fs
  • NP_001393813.1:p.Lys364fs
  • NP_001393814.1:p.Lys360fs
  • NP_001393815.1:p.Lys350fs
  • NP_001393816.1:p.Lys337fs
  • NP_001393817.1:p.Lys337fs
  • NP_001393818.1:p.Lys337fs
  • NP_001393819.1:p.Lys337fs
  • NP_001393820.1:p.Lys337fs
  • NP_001393821.1:p.Lys337fs
  • NP_001393822.1:p.Lys337fs
  • NP_001393823.1:p.Lys337fs
  • NP_001393824.1:p.Lys337fs
  • NP_001393825.1:p.Lys337fs
  • NP_001393826.1:p.Lys337fs
  • NP_001393827.1:p.Lys337fs
  • NP_001393828.1:p.Lys337fs
  • NP_001393829.1:p.Lys317fs
  • NP_001393830.1:p.Lys314fs
  • NP_001393831.1:p.Lys314fs
  • NP_001393832.1:p.Lys366fs
  • NP_001393833.1:p.Lys301fs
  • NP_001393834.1:p.Lys301fs
  • NP_001393835.1:p.Lys285fs
  • NP_001393836.1:p.Lys285fs
  • NP_001393837.1:p.Lys337fs
  • NP_001393838.1:p.Lys281fs
  • NP_001393839.1:p.Lys337fs
  • NP_001393840.1:p.Lys215fs
  • LRG_161t1:c.1412_1415del
  • LRG_161:g.26757_26760del
  • LRG_161p1:p.Lys472Argfs
  • NC_000007.13:g.6026981_6026984del
  • NM_000535.5:c.1412_1415delAGAA
  • NR_003085.2:n.1494_1497delAGAA
  • NR_136154.1:n.1502_1505del
Protein change:
K161fs
Molecular consequence:
  • NM_000535.7:c.1415_1418del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001018040.1:c.1007_1010delAGAA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322003.2:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322004.2:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322005.2:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322006.2:c.1259_1262del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322007.2:c.1097_1100del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322008.2:c.1097_1100del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322009.2:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322010.2:c.854_857del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322011.2:c.482_485del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322012.2:c.482_485del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322013.2:c.842_845del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322014.2:c.1415_1418del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322015.2:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406866.1:c.1601_1604del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406868.1:c.1439_1442del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406869.1:c.1307_1310del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406870.1:c.1259_1262del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406871.1:c.1415_1418del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406872.1:c.1415_1418del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406873.1:c.1217_1220del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406874.1:c.1247_1250del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406875.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406876.1:c.1097_1100del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406877.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406878.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406879.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406880.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406881.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406882.1:c.1106_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406883.1:c.1097_1100del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406884.1:c.1091_1094del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406885.1:c.1079_1082del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406886.1:c.1049_1052del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406887.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406888.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406889.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406890.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406891.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406892.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406893.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406894.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406895.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406896.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406897.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406898.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406899.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406900.1:c.950_953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406901.1:c.941_944del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406902.1:c.941_944del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406903.1:c.1097_1100del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406904.1:c.902_905del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406905.1:c.902_905del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406906.1:c.854_857del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406907.1:c.854_857del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406908.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406909.1:c.842_845del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406910.1:c.1010_1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406911.1:c.644_647del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406912.1:c.804-4359_804-4356del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_136154.1:n.1502_1505del - 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
SCV004185944Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Pathogenic
(Oct 9, 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., SCV004185944.1

#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: Dec 30, 2023