NM_000535.7(PMS2):c.251C>G (p.Thr84Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 3, 2022
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:: RCV001705171.3

Allele description [Variation Report for NM_000535.7(PMS2):c.251C>G (p.Thr84Ser)]

NM_000535.7(PMS2):c.251C>G (p.Thr84Ser)

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.251C>G (p.Thr84Ser)

HGVS:

NC_000007.14:g.6003792G>C
NG_008466.1:g.10315C>G
NM_000535.7:c.251C>GMANE SELECT
NM_001322003.2:c.-155C>G
NM_001322004.2:c.-155C>G
NM_001322005.2:c.-155C>G
NM_001322006.2:c.251C>G
NM_001322007.2:c.35+180C>G
NM_001322008.2:c.35+180C>G
NM_001322009.2:c.-155C>G
NM_001322010.2:c.-155C>G
NM_001322011.2:c.-634C>G
NM_001322012.2:c.-634C>G
NM_001322013.2:c.-155C>G
NM_001322014.2:c.251C>G
NM_001322015.2:c.-234C>G
NP_000526.2:p.Thr84Ser
NP_001308935.1:p.Thr84Ser
NP_001308943.1:p.Thr84Ser
LRG_161t1:c.251C>G
LRG_161:g.10315C>G
NC_000007.13:g.6043423G>C
NM_000535.5:c.251C>G
NM_000535.6:c.251C>G
NR_136154.1:n.338C>G

Protein change:

T84S

Links:

dbSNP: rs864622274

NCBI 1000 Genomes Browser:

rs864622274

Molecular consequence:

NM_001322003.2:c.-155C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-155C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-155C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-155C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-155C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-634C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-634C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-155C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-234C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.35+180C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+180C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.251C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.251C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.251C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.338C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000565381	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 3, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000565381

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 3, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000565381.4

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Observed in an individual with pediatric-onset acute lymphocytic leukemia (Zhang 2015); This variant is associated with the following publications: (PMID: 26580448, 11574484, 27535533)

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

Last Updated: Sep 29, 2024

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