NM_000535.7(PMS2):c.88C>A (p.Gln30Lys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 16, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001550352.5

Allele description [Variation Report for NM_000535.7(PMS2):c.88C>A (p.Gln30Lys)]

NM_000535.7(PMS2):c.88C>A (p.Gln30Lys)

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>A (p.Gln30Lys)

HGVS:

NC_000007.14:g.6005967G>T
NG_008466.1:g.8140C>A
NG_050738.1:g.1717G>T
NM_000535.7:c.88C>AMANE SELECT
NM_001322003.2:c.-318C>A
NM_001322004.2:c.-242-1909C>A
NM_001322005.2:c.-318C>A
NM_001322006.2:c.88C>A
NM_001322007.2:c.-128C>A
NM_001322008.2:c.-52-1909C>A
NM_001322009.2:c.-318C>A
NM_001322010.2:c.-242-1909C>A
NM_001322011.2:c.-797C>A
NM_001322012.2:c.-797C>A
NM_001322013.2:c.-318C>A
NM_001322014.2:c.88C>A
NM_001322015.2:c.-397C>A
NP_000526.2:p.Gln30Lys
NP_001308935.1:p.Gln30Lys
NP_001308943.1:p.Gln30Lys
LRG_161t1:c.88C>A
LRG_161:g.8140C>A
NC_000007.13:g.6045598G>T
NM_000535.5:c.88C>A
NM_000535.6:c.88C>A
NR_136154.1:n.175C>A

Protein change:

Q30K

Links:

dbSNP: rs141577476

NCBI 1000 Genomes Browser:

rs141577476

Molecular consequence:

NM_001322003.2:c.-318C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-318C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-128C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-318C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-797C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-797C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-318C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-397C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1909C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1909C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1909C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.88C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.88C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.88C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.175C>A - 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
SCV001770665	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 16, 2021)	germline	clinical testing	Citation Link,
SCV002046217	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Sep 16, 2020)	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

SCV001770665

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 16, 2021)

germline

clinical testing

Citation Link,

SCV002046217

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Sep 16, 2020)

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	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV001770665.3

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

Description

Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; 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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002046217.1

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

#	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: Oct 13, 2024

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