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NM_000535.7(PMS2):c.2547C>T (p.Thr849=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 10, 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:
RCV002433271.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2547C>T (p.Thr849=)]

NM_000535.7(PMS2):c.2547C>T (p.Thr849=)

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.2547C>T (p.Thr849=)
HGVS:
  • NC_000007.14:g.5973441G>A
  • NG_008466.1:g.40666C>T
  • NM_000535.7:c.2547C>TMANE SELECT
  • NM_001018040.1:c.2142C>T
  • NM_001322003.2:c.2142C>T
  • NM_001322004.2:c.2142C>T
  • NM_001322005.2:c.2142C>T
  • NM_001322006.2:c.2391C>T
  • NM_001322007.2:c.2229C>T
  • NM_001322008.2:c.2229C>T
  • NM_001322009.2:c.2175C>T
  • NM_001322010.2:c.1986C>T
  • NM_001322011.2:c.1614C>T
  • NM_001322012.2:c.1614C>T
  • NM_001322013.2:c.1974C>T
  • NM_001322014.2:c.2580C>T
  • NM_001322015.2:c.2238C>T
  • NM_001406866.1:c.2733C>T
  • NM_001406868.1:c.2571C>T
  • NM_001406869.1:c.2439C>T
  • NM_001406870.1:c.2424C>T
  • NM_001406871.1:c.2403C>T
  • NM_001406872.1:c.2379C>T
  • NM_001406873.1:c.2349C>T
  • NM_001406874.1:c.2379C>T
  • NM_001406875.1:c.2271C>T
  • NM_001406876.1:c.2262C>T
  • NM_001406877.1:c.2238C>T
  • NM_001406878.1:c.2238C>T
  • NM_001406879.1:c.2238C>T
  • NM_001406880.1:c.2238C>T
  • NM_001406881.1:c.2238C>T
  • NM_001406882.1:c.2238C>T
  • NM_001406883.1:c.2229C>T
  • NM_001406884.1:c.2223C>T
  • NM_001406885.1:c.2211C>T
  • NM_001406886.1:c.2181C>T
  • NM_001406887.1:c.2175C>T
  • NM_001406888.1:c.2175C>T
  • NM_001406889.1:c.2142C>T
  • NM_001406890.1:c.2142C>T
  • NM_001406891.1:c.2142C>T
  • NM_001406892.1:c.2142C>T
  • NM_001406893.1:c.2142C>T
  • NM_001406894.1:c.2142C>T
  • NM_001406895.1:c.2142C>T
  • NM_001406896.1:c.2142C>T
  • NM_001406897.1:c.2142C>T
  • NM_001406898.1:c.2142C>T
  • NM_001406899.1:c.2142C>T
  • NM_001406900.1:c.2082C>T
  • NM_001406901.1:c.2073C>T
  • NM_001406902.1:c.2073C>T
  • NM_001406903.1:c.2061C>T
  • NM_001406904.1:c.2034C>T
  • NM_001406905.1:c.2034C>T
  • NM_001406906.1:c.1986C>T
  • NM_001406907.1:c.1986C>T
  • NM_001406908.1:c.1974C>T
  • NM_001406909.1:c.1974C>T
  • NM_001406910.1:c.1830C>T
  • NM_001406911.1:c.1776C>T
  • NM_001406912.1:c.1344C>T
  • NP_000526.1:p.Thr849=
  • NP_000526.2:p.Thr849=
  • NP_001018050.1:p.Thr714=
  • NP_001308932.1:p.Thr714=
  • NP_001308933.1:p.Thr714=
  • NP_001308934.1:p.Thr714=
  • NP_001308935.1:p.Thr797=
  • NP_001308936.1:p.Thr743=
  • NP_001308937.1:p.Thr743=
  • NP_001308938.1:p.Thr725=
  • NP_001308939.1:p.Thr662=
  • NP_001308940.1:p.Thr538=
  • NP_001308941.1:p.Thr538=
  • NP_001308942.1:p.Thr658=
  • NP_001308943.1:p.Thr860=
  • NP_001308944.1:p.Thr746=
  • NP_001393795.1:p.Thr911=
  • NP_001393797.1:p.Thr857=
  • NP_001393798.1:p.Thr813=
  • NP_001393799.1:p.Thr808=
  • NP_001393800.1:p.Thr801=
  • NP_001393801.1:p.Thr793=
  • NP_001393802.1:p.Thr783=
  • NP_001393803.1:p.Thr793=
  • NP_001393804.1:p.Thr757=
  • NP_001393805.1:p.Thr754=
  • NP_001393806.1:p.Thr746=
  • NP_001393807.1:p.Thr746=
  • NP_001393808.1:p.Thr746=
  • NP_001393809.1:p.Thr746=
  • NP_001393810.1:p.Thr746=
  • NP_001393811.1:p.Thr746=
  • NP_001393812.1:p.Thr743=
  • NP_001393813.1:p.Thr741=
  • NP_001393814.1:p.Thr737=
  • NP_001393815.1:p.Thr727=
  • NP_001393816.1:p.Thr725=
  • NP_001393817.1:p.Thr725=
  • NP_001393818.1:p.Thr714=
  • NP_001393819.1:p.Thr714=
  • NP_001393820.1:p.Thr714=
  • NP_001393821.1:p.Thr714=
  • NP_001393822.1:p.Thr714=
  • NP_001393823.1:p.Thr714=
  • NP_001393824.1:p.Thr714=
  • NP_001393825.1:p.Thr714=
  • NP_001393826.1:p.Thr714=
  • NP_001393827.1:p.Thr714=
  • NP_001393828.1:p.Thr714=
  • NP_001393829.1:p.Thr694=
  • NP_001393830.1:p.Thr691=
  • NP_001393831.1:p.Thr691=
  • NP_001393832.1:p.Thr687=
  • NP_001393833.1:p.Thr678=
  • NP_001393834.1:p.Thr678=
  • NP_001393835.1:p.Thr662=
  • NP_001393836.1:p.Thr662=
  • NP_001393837.1:p.Thr658=
  • NP_001393838.1:p.Thr658=
  • NP_001393839.1:p.Thr610=
  • NP_001393840.1:p.Thr592=
  • NP_001393841.1:p.Thr448=
  • LRG_161t1:c.2547C>T
  • LRG_161:g.40666C>T
  • LRG_161p1:p.Thr849=
  • NC_000007.13:g.6013072G>A
  • NM_000535.5:c.2547C>T
  • NR_003085.2:n.2629C>T
  • NR_136154.1:n.2591C>T
Molecular consequence:
  • NR_136154.1:n.2591C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.2547C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001018040.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322003.2:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322004.2:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322005.2:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322006.2:c.2391C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322007.2:c.2229C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322008.2:c.2229C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322009.2:c.2175C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322010.2:c.1986C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322011.2:c.1614C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322012.2:c.1614C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322013.2:c.1974C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322014.2:c.2580C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322015.2:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406866.1:c.2733C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406868.1:c.2571C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406869.1:c.2439C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406870.1:c.2424C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406871.1:c.2403C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406872.1:c.2379C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406873.1:c.2349C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406874.1:c.2379C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406875.1:c.2271C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406876.1:c.2262C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406877.1:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406878.1:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406879.1:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406880.1:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406881.1:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406882.1:c.2238C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406883.1:c.2229C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406884.1:c.2223C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406885.1:c.2211C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406886.1:c.2181C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406887.1:c.2175C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406888.1:c.2175C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406889.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406890.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406891.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406892.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406893.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406894.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406895.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406896.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406897.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406898.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406899.1:c.2142C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406900.1:c.2082C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406901.1:c.2073C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406902.1:c.2073C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406903.1:c.2061C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406904.1:c.2034C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406905.1:c.2034C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406906.1:c.1986C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406907.1:c.1986C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406908.1:c.1974C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406909.1:c.1974C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406910.1:c.1830C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406911.1:c.1776C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406912.1:c.1344C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002740623Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Apr 10, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002740623.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Sep 29, 2024