NM_000535.7(PMS2):c.1621= (p.Lys541=) AND Lynch syndrome

Clinical significance:Benign (Last evaluated: Sep 5, 2013)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000030365.4

Allele description [Variation Report for NM_000535.7(PMS2):c.1621= (p.Lys541=)]

NM_000535.7(PMS2):c.1621= (p.Lys541=)

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.1621= (p.Lys541=)
Other names:
p.E541K:GAA>AAA
HGVS:
  • NC_000007.14:g.5987144=
  • NG_008466.1:g.26963G>A
  • NM_000535.7:c.1621=MANE SELECT
  • NM_001322003.2:c.1216=
  • NM_001322004.2:c.1216=
  • NM_001322005.2:c.1216=
  • NM_001322006.2:c.1465=
  • NM_001322007.1:c.1303=
  • NM_001322008.2:c.1303=
  • NM_001322009.2:c.1216=
  • NM_001322010.2:c.1060=
  • NM_001322011.2:c.688=
  • NM_001322012.2:c.688=
  • NM_001322013.2:c.1048=
  • NM_001322014.2:c.1621=
  • NM_001322015.2:c.1312=
  • NP_000526.2:p.Lys541=
  • NP_001308932.1:p.Lys406=
  • NP_001308933.1:p.Lys406=
  • NP_001308934.1:p.Lys406=
  • NP_001308935.1:p.Lys489=
  • NP_001308936.1:p.Lys435=
  • NP_001308937.1:p.Lys435=
  • NP_001308938.1:p.Lys406=
  • NP_001308939.1:p.Lys354=
  • NP_001308940.1:p.Lys230=
  • NP_001308941.1:p.Lys230=
  • NP_001308942.1:p.Lys350=
  • NP_001308943.1:p.Lys541=
  • NP_001308944.1:p.Lys438=
  • LRG_161t1:c.1621G>A
  • LRG_161:g.26963G>A
  • NC_000007.13:g.6026775=
  • NC_000007.13:g.6026775T=
  • NR_136154.1:n.1708=
  • p.Lys541Glu
  • p.Lys541Lys
Links:
dbSNP: rs2228006
NCBI 1000 Genomes Browser:
rs2228006
Molecular consequence:
  • NM_000535.7:c.1621= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322003.2:c.1216= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322004.2:c.1216= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322005.2:c.1216= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322006.2:c.1465= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322007.1:c.1303= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322008.2:c.1303= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322009.2:c.1216= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322010.2:c.1060= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322011.2:c.688= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322012.2:c.688= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322013.2:c.1048= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322014.2:c.1621= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NM_001322015.2:c.1312= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NR_136154.1:n.1708= - no sequence alteration - [Sequence Ontology: SO:0002073]
  • NR_136154.1:n.1708= - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Lynch syndrome
Synonyms:
Familial nonpolyposis colon cancer
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100; OMIM: PS120435

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000053032Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
benign
(Aug 18, 2011)
not providedclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link,

SCV000108304International Society for Gastrointestinal Hereditary Tumours (InSiGHT)reviewed by expert panel
no known pathogenicity
(Sep 5, 2013)
germlineresearch

Citation Link

Description

SCV000108304

Summary from all submissions

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

Citations

PubMed

Common variants in mismatch repair genes and risk of invasive ovarian cancer.

Song H, Ramus SJ, Quaye L, DiCioccio RA, Tyrer J, Lomas E, Shadforth D, Hogdall E, Hogdall C, McGuire V, Whittemore AS, Easton DF, Ponder BA, Kjaer SK, Pharoah PD, Gayther SA.

Carcinogenesis. 2006 Nov;27(11):2235-42. Epub 2006 Jun 13.

PubMed [citation]
PMID:
16774946

Mismatch repair gene PMS2: disease-causing germline mutations are frequent in patients whose tumors stain negative for PMS2 protein, but paralogous genes obscure mutation detection and interpretation.

Nakagawa H, Lockman JC, Frankel WL, Hampel H, Steenblock K, Burgart LJ, Thibodeau SN, de la Chapelle A.

Cancer Res. 2004 Jul 15;64(14):4721-7.

PubMed [citation]
PMID:
15256438
See all PubMed Citations (7)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000053032.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

Converted during submission to Benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot providednot providednot providednot providednot providednot providednot providednot provided

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000108304.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

MAF >1%

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

Last Updated: Jun 14, 2021

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