NM_000535.7(PMS2):c.65C>G (p.Ser22Ter) 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:: RCV003449728.1

Allele description [Variation Report for NM_000535.7(PMS2):c.65C>G (p.Ser22Ter)]

NM_000535.7(PMS2):c.65C>G (p.Ser22Ter)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.65C>G (p.Ser22Ter)

HGVS:

NC_000007.14:g.6005990G>C
NG_008466.1:g.8117C>G
NG_050738.1:g.1740G>C
NM_000535.7:c.65C>GMANE SELECT
NM_001322003.2:c.-341C>G
NM_001322004.2:c.-242-1932C>G
NM_001322005.2:c.-341C>G
NM_001322006.2:c.65C>G
NM_001322007.2:c.-151C>G
NM_001322008.2:c.-52-1932C>G
NM_001322009.2:c.-341C>G
NM_001322010.2:c.-242-1932C>G
NM_001322011.2:c.-820C>G
NM_001322012.2:c.-820C>G
NM_001322013.2:c.-341C>G
NM_001322014.2:c.65C>G
NM_001322015.2:c.-420C>G
NP_000526.2:p.Ser22Ter
NP_001308935.1:p.Ser22Ter
NP_001308943.1:p.Ser22Ter
LRG_161t1:c.65C>G
LRG_161:g.8117C>G
NC_000007.13:g.6045621G>C
NM_000535.5:c.65C>G
NR_136154.1:n.152C>G

Protein change:

S22*

Links:

dbSNP: rs767028531

NCBI 1000 Genomes Browser:

rs767028531

Molecular consequence:

NM_001322003.2:c.-341C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-341C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-151C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-341C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-820C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-820C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-341C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-420C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1932C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1932C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1932C>G - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.152C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.65C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001322006.2:c.65C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001322014.2:c.65C>G - nonsense - [Sequence Ontology: SO:0001587]

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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RecName: Full=Palladin
RecName: Full=Palladin
gi|158564030|sp|Q9ET54.2|PALLD_MOUS

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187790	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

SCV004187790

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

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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., SCV004187790.1

#	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 termination codon and is 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

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