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

Recent activity

Clear Turn Off Turn On

auxin response factor 18 [Sesamum indicum]
auxin response factor 18 [Sesamum indicum]
gi|747074654|ref|XP_011084326.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187699	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Sep 19, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187699

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Sep 19, 2023)

unknown

clinical testing

Citation Link

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

Details of each submission

From Myriad Genetics, Inc., SCV004187699.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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

#	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: May 1, 2024

ClinVar

Relating variation to medicine