NM_000535.7(PMS2):c.51_55del (p.Ile18fs) AND Lynch syndrome 4

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Sep 18, 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:: RCV003454163.2

Allele description [Variation Report for NM_000535.7(PMS2):c.51_55del (p.Ile18fs)]

NM_000535.7(PMS2):c.51_55del (p.Ile18fs)

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.51_55del (p.Ile18fs)

HGVS:

NC_000007.14:g.6006000_6006004del
NG_008466.1:g.8103_8107del
NG_050738.1:g.1750_1754del
NM_000535.7:c.51_55delMANE SELECT
NM_001018040.1:c.-355_-351delTATTG
NM_001322003.2:c.-355_-351del
NM_001322004.2:c.-242-1946_-242-1942del
NM_001322005.2:c.-355_-351del
NM_001322006.2:c.51_55del
NM_001322007.2:c.-165_-161del
NM_001322008.2:c.-52-1946_-52-1942del
NM_001322009.2:c.-355_-351del
NM_001322010.2:c.-242-1946_-242-1942del
NM_001322011.2:c.-834_-830del
NM_001322012.2:c.-834_-830del
NM_001322013.2:c.-355_-351del
NM_001322014.2:c.51_55del
NM_001322015.2:c.-434_-430del
NM_001406866.1:c.237_241delTATTG
NM_001406868.1:c.51_55delTATTG
NM_001406869.1:c.51_55delTATTG
NM_001406870.1:c.51_55delTATTG
NM_001406871.1:c.51_55delTATTG
NM_001406872.1:c.51_55delTATTG
NM_001406873.1:c.51_55delTATTG
NM_001406874.1:c.51_55delTATTG
NM_001406875.1:c.-434_-430delTATTG
NM_001406876.1:c.-165_-161delTATTG
NM_001406877.1:c.-434_-430delTATTG
NM_001406878.1:c.-434_-430delTATTG
NM_001406880.1:c.-381_-377delTATTG
NM_001406882.1:c.-434_-430delTATTG
NM_001406883.1:c.-165_-161delTATTG
NM_001406884.1:c.51_55delTATTG
NM_001406885.1:c.51_55delTATTG
NM_001406886.1:c.51_55delTATTG
NM_001406887.1:c.-355_-351delTATTG
NM_001406888.1:c.-302_-298delTATTG
NM_001406889.1:c.-302_-298delTATTG
NM_001406890.1:c.-345_-341delTATTG
NM_001406891.1:c.-355_-351delTATTG
NM_001406892.1:c.-302_-298delTATTG
NM_001406893.1:c.-355_-351delTATTG
NM_001406894.1:c.-302_-298delTATTG
NM_001406896.1:c.-165_-161delTATTG
NM_001406897.1:c.-355_-351delTATTG
NM_001406898.1:c.-355_-351delTATTG
NM_001406899.1:c.-302_-298delTATTG
NM_001406900.1:c.-331_-327delTATTG
NM_001406901.1:c.-165_-161delTATTG
NM_001406902.1:c.-165_-161delTATTG
NM_001406903.1:c.-165_-161delTATTG
NM_001406904.1:c.-302_-298delTATTG
NM_001406905.1:c.-355_-351delTATTG
NM_001406906.1:c.-355_-351delTATTG
NM_001406907.1:c.-302_-298delTATTG
NM_001406908.1:c.-355_-351delTATTG
NM_001406909.1:c.-302_-298delTATTG
NM_001406910.1:c.-355_-351delTATTG
NM_001406912.1:c.51_55delTATTG
NP_000526.1:p.Ile18Serfs
NP_000526.2:p.Ile18fs
NP_001308935.1:p.Ile18fs
NP_001308943.1:p.Ile18fs
NP_001393795.1:p.Ile80Serfs
NP_001393797.1:p.Ile18Serfs
NP_001393798.1:p.Ile18Serfs
NP_001393799.1:p.Ile18Serfs
NP_001393800.1:p.Ile18Serfs
NP_001393801.1:p.Ile18Serfs
NP_001393802.1:p.Ile18Serfs
NP_001393803.1:p.Ile18Serfs
NP_001393813.1:p.Ile18Serfs
NP_001393814.1:p.Ile18Serfs
NP_001393815.1:p.Ile18Serfs
NP_001393841.1:p.Ile18Serfs
LRG_161t1:c.51_55del
LRG_161:g.8103_8107del
LRG_161p1:p.Ile18Serfs
NC_000007.13:g.6045631_6045635del
NM_000535.5:c.51_55delTATTG
NM_000535.7:c.51_55delTATTGMANE SELECT
NR_003085.2:n.133_137delTATTG
NR_136154.1:n.138_142del

Protein change:

I18fs

Molecular consequence:

NM_001322003.2:c.-355_-351del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-355_-351del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-165_-161del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-355_-351del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-834_-830del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-834_-830del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-355_-351del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-434_-430del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.51_55del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.51_55del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.51_55del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406866.1:c.237_241delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406868.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406869.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406870.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406871.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406872.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406873.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406874.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406884.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406885.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406886.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406912.1:c.51_55delTATTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.-242-1946_-242-1942del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1946_-52-1942del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1946_-242-1942del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.138_142del - 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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cytochrome P450 4F11 [Homo sapiens]
cytochrome P450 4F11 [Homo sapiens]
gi|193083178|ref|NP_067010.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004188636	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Sep 18, 2023)	unknown	clinical testing	Citation Link,
SCV004207892	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 3, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004188636

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Sep 18, 2023)

unknown

clinical testing

Citation Link,

SCV004207892

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 3, 2022)

unknown

clinical testing

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

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

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., SCV004188636.1

#	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

From Baylor Genetics, SCV004207892.1

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

#	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: Sep 29, 2024

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