NM_000535.6(PMS2):c.2324A>G (p.Asn775Ser) AND not specified

Clinical significance:Benign (Last evaluated: Sep 24, 2015)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000079108.9

Allele description

NM_000535.6(PMS2):c.2324A>G (p.Asn775Ser)

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_000535.6(PMS2):c.2324A>G (p.Asn775Ser)
Other names:
p.N775S:AAC>AGC
HGVS:
  • NC_000007.14:g.5977709T>C
  • NG_008466.1:g.36398A>G
  • NM_000535.6:c.2324A>G
  • NP_000526.2:p.Asn775Ser
  • LRG_161t1:c.2324A>G
  • LRG_161:g.36398A>G
  • LRG_161p1:p.Asn775Ser
  • NC_000007.13:g.6017340T>C
  • NM_000535.5:c.2324A>G
  • NP_000526.1:p.Asn775Ser
  • NR_136154.1:n.2368A>G
  • P54278:p.Asn775Ser
  • p.N775S
Protein change:
N775S
Links:
UniProtKB: P54278#VAR_016135; dbSNP: rs17420802
NCBI 1000 Genomes Browser:
rs17420802
Allele Frequency:
0.00037(C)
Molecular consequence:
  • NM_000535.6:c.2324A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2368A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
24

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000086053ITMIno assertion providednot providedgermlinereference population

PubMed (1)
[See all records that cite this PMID]

SCV000110977Emory Genetics Laboratory,Emory Universitycriteria provided, single submitter
Benign
(Sep 24, 2015)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000171039GeneDxcriteria provided, single submitter
Benign
(Jan 16, 2014)
germlineclinical testing

Citation Link,

SCV000257310Mayo Clinic Genetic Testing Laboratories,Mayo Clinicno assertion criteria providedBenignunknownresearch

SCV000304729PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Description

Please see associated publication for description of ethnicities

SCV000086053

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknown1not providednot providednot providednot providedresearch
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown24not providednot providednot providednot providedclinical testing
Africangermlineunknownnot providednot providednot provided43not providedreference population
African_Europeangermlineunknownnot providednot providednot provided46not providedreference population
Central_Asiangermlineunknownnot providednot providednot provided50not providedreference population
East_Asiangermlineunknownnot providednot providednot provided62not providedreference population
Europeangermlineunknownnot providednot providednot provided331not providedreference population
Hispanicgermlineunknownnot providednot providednot provided118not providedreference population
Whole_cohortgermlineunknownnot providednot providednot provided681not providedreference population

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]
PMID:
24728327
PMCID:
PMC3984285

Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.

Bean LJ, Tinker SW, da Silva C, Hegde MR.

Hum Mutat. 2013 Sep;34(9):1183-8. doi: 10.1002/humu.22364. Epub 2013 Aug 5.

PubMed [citation]
PMID:
23757202
See all PubMed Citations (3)

Details of each submission

From ITMI, SCV000086053.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Africannot providednot providednot providedreference population PubMed (1)
2African_Europeannot providednot providednot providedreference population PubMed (1)
3Central_Asiannot providednot providednot providedreference population PubMed (1)
4East_Asiannot providednot providednot providedreference population PubMed (1)
5Europeannot providednot providednot providedreference population PubMed (1)
6Hispanicnot providednot providednot providedreference population PubMed (1)
7Whole_cohortnot providednot providednot providedreference population PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown43not provideddiscoverynot provided0.0241not providednot provided
2germlineunknown46not provideddiscoverynot provided0not providednot provided
3germlineunknown50not provideddiscoverynot provided0not providednot provided
4germlineunknown62not provideddiscoverynot provided0not providednot provided
5germlineunknown331not provideddiscoverynot provided0.0066not providednot provided
6germlineunknown118not provideddiscoverynot provided0not providednot provided
7germlineunknown681not provideddiscoverynot provided0.0055not providednot provided

From Emory Genetics Laboratory,Emory University, SCV000110977.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided24not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided24not providednot providednot provided

From GeneDx, SCV000171039.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Mayo Clinic Genetic Testing Laboratories,Mayo Clinic, SCV000257310.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot provided1not providednot providednot provided

From PreventionGenetics, SCV000304729.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 3, 2017

Support Center