NM_000535.7(PMS2):c.88C>T (p.Gln30Ter) AND Mismatch repair cancer syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 3, 2019
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:: RCV001197302.3

Allele description [Variation Report for NM_000535.7(PMS2):c.88C>T (p.Gln30Ter)]

NM_000535.7(PMS2):c.88C>T (p.Gln30Ter)

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.88C>T (p.Gln30Ter)

HGVS:

NC_000007.14:g.6005967G>A
NG_008466.1:g.8140C>T
NG_050738.1:g.1717G>A
NM_000535.7:c.88C>TMANE SELECT
NM_001322003.2:c.-318C>T
NM_001322004.2:c.-242-1909C>T
NM_001322005.2:c.-318C>T
NM_001322006.2:c.88C>T
NM_001322007.2:c.-128C>T
NM_001322008.2:c.-52-1909C>T
NM_001322009.2:c.-318C>T
NM_001322010.2:c.-242-1909C>T
NM_001322011.2:c.-797C>T
NM_001322012.2:c.-797C>T
NM_001322013.2:c.-318C>T
NM_001322014.2:c.88C>T
NM_001322015.2:c.-397C>T
NP_000526.2:p.Gln30Ter
NP_001308935.1:p.Gln30Ter
NP_001308943.1:p.Gln30Ter
LRG_161t1:c.88C>T
LRG_161:g.8140C>T
NC_000007.13:g.6045598G>A
NM_000535.5:c.88C>T
NM_000535.6:c.88C>T
NR_136154.1:n.175C>T
p.Gln30X
p.Q30*

Protein change:

Q30*

Links:

dbSNP: rs141577476

NCBI 1000 Genomes Browser:

rs141577476

Molecular consequence:

NM_001322003.2:c.-318C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-318C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-128C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-318C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-797C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-797C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-318C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-397C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1909C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1909C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1909C>T - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.175C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.88C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322006.2:c.88C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322014.2:c.88C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Mismatch repair cancer syndrome 1 (MMRCS1)
Synonyms:: BRAIN TUMOR-POLYPOSIS SYNDROME 1; BTP1 SYNDROME; CHILDHOOD CANCER SYNDROME; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010159; MedGen: C5399763; Orphanet: 252202; OMIM: 276300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001367965	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 3, 2019)	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

SCV001367965

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 3, 2019)

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	yes	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 Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001367965.2

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

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP3,PP5.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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