NM_000535.7(PMS2):c.312del (p.Phe104fs) 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:: RCV003449665.1

Allele description [Variation Report for NM_000535.7(PMS2):c.312del (p.Phe104fs)]

NM_000535.7(PMS2):c.312del (p.Phe104fs)

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.312del (p.Phe104fs)

HGVS:

NC_000007.14:g.6003734del
NG_008466.1:g.10376del
NM_000535.7:c.312delMANE SELECT
NM_001322003.2:c.-94del
NM_001322004.2:c.-94del
NM_001322005.2:c.-94del
NM_001322006.2:c.312del
NM_001322007.2:c.35+241del
NM_001322008.2:c.35+241del
NM_001322009.2:c.-94del
NM_001322010.2:c.-94del
NM_001322011.2:c.-573del
NM_001322012.2:c.-573del
NM_001322013.2:c.-94del
NM_001322014.2:c.312del
NM_001322015.2:c.-173del
NP_000526.2:p.Phe104fs
NP_001308935.1:p.Phe104fs
NP_001308943.1:p.Phe104fs
LRG_161t1:c.312del
LRG_161:g.10376del
NC_000007.13:g.6043362del
NC_000007.13:g.6043365del
NM_000535.5:c.312del
NR_136154.1:n.399del

Protein change:

F104fs

Links:

dbSNP: rs1785372371

NCBI 1000 Genomes Browser:

rs1785372371

Molecular consequence:

NM_001322003.2:c.-94del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-94del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-94del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-94del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-94del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-573del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-573del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-94del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-173del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.312del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.312del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.312del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.35+241del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+241del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.399del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187752	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

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187752

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

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., SCV004187752.1

#	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: Sep 29, 2024

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