NM_000535.7(PMS2):c.265A>G (p.Thr89Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 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:: RCV002269447.2

Allele description [Variation Report for NM_000535.7(PMS2):c.265A>G (p.Thr89Ala)]

NM_000535.7(PMS2):c.265A>G (p.Thr89Ala)

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.265A>G (p.Thr89Ala)

HGVS:

NC_000007.14:g.6003778T>C
NG_008466.1:g.10329A>G
NM_000535.7:c.265A>GMANE SELECT
NM_001322003.2:c.-141A>G
NM_001322004.2:c.-141A>G
NM_001322005.2:c.-141A>G
NM_001322006.2:c.265A>G
NM_001322007.2:c.35+194A>G
NM_001322008.2:c.35+194A>G
NM_001322009.2:c.-141A>G
NM_001322010.2:c.-141A>G
NM_001322011.2:c.-620A>G
NM_001322012.2:c.-620A>G
NM_001322013.2:c.-141A>G
NM_001322014.2:c.265A>G
NM_001322015.2:c.-220A>G
NP_000526.2:p.Thr89Ala
NP_001308935.1:p.Thr89Ala
NP_001308943.1:p.Thr89Ala
LRG_161t1:c.265A>G
LRG_161:g.10329A>G
NC_000007.13:g.6043409T>C
NM_000535.5:c.265A>G
NR_136154.1:n.352A>G

Protein change:

T89A

Links:

dbSNP: rs2128827539

NCBI 1000 Genomes Browser:

rs2128827539

Molecular consequence:

NM_001322003.2:c.-141A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-141A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-141A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-141A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-141A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-620A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-620A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-141A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-220A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.35+194A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+194A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.265A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.265A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.265A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.352A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Porphyromonas gulae strain COT-052 OH3856 contig_7, whole genome shotgun sequenc...
Porphyromonas gulae strain COT-052 OH3856 contig_7, whole genome shotgun sequence
gi|746374171|ref|NZ_JRAT01000007.1| WGS:NZ_JRAT01|contig_7

Nucleotide
MKI67 marker of proliferation Ki-67 [Homo sapiens]
MKI67 marker of proliferation Ki-67 [Homo sapiens]
Gene ID:4288

Gene
Gene Links for GEO Profiles (Select 30482629) (1)
Gene
Related DataSets for GEO Profiles (Select 30482629) (1)
GEO DataSets
Hepatitis B surface antigen effect on hepatoma cell line
Hepatitis B surface antigen effect on hepatoma cell line
Accession: GDS2339

GEO DataSets

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002552665	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jan 25, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002552665

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jan 25, 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, SCV002552665.2

#	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 supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 11574484)

#	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: May 1, 2024

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