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NM_000535.7(PMS2):c.2119T>A (p.Tyr707Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 18, 2023
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:
RCV004518716.1

Allele description [Variation Report for NM_000535.7(PMS2):c.2119T>A (p.Tyr707Asn)]

NM_000535.7(PMS2):c.2119T>A (p.Tyr707Asn)

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.2119T>A (p.Tyr707Asn)
HGVS:
  • NC_000007.14:g.5982879A>T
  • NG_008466.1:g.31228T>A
  • NM_000535.7:c.2119T>AMANE SELECT
  • NM_001018040.1:c.1714T>A
  • NM_001322003.2:c.1714T>A
  • NM_001322004.2:c.1714T>A
  • NM_001322005.2:c.1714T>A
  • NM_001322006.2:c.1963T>A
  • NM_001322007.2:c.1801T>A
  • NM_001322008.2:c.1801T>A
  • NM_001322009.2:c.1714T>A
  • NM_001322010.2:c.1558T>A
  • NM_001322011.2:c.1186T>A
  • NM_001322012.2:c.1186T>A
  • NM_001322013.2:c.1546T>A
  • NM_001322014.2:c.2119T>A
  • NM_001322015.2:c.1810T>A
  • NM_001406866.1:c.2305T>A
  • NM_001406868.1:c.2143T>A
  • NM_001406869.1:c.2011T>A
  • NM_001406870.1:c.1963T>A
  • NM_001406871.1:c.2119T>A
  • NM_001406872.1:c.2006+3880T>A
  • NM_001406873.1:c.1921T>A
  • NM_001406874.1:c.1951T>A
  • NM_001406875.1:c.1810T>A
  • NM_001406876.1:c.1801T>A
  • NM_001406877.1:c.1810T>A
  • NM_001406878.1:c.1810T>A
  • NM_001406879.1:c.1810T>A
  • NM_001406880.1:c.1810T>A
  • NM_001406881.1:c.1810T>A
  • NM_001406882.1:c.1810T>A
  • NM_001406883.1:c.1801T>A
  • NM_001406884.1:c.1795T>A
  • NM_001406885.1:c.1783T>A
  • NM_001406886.1:c.1753T>A
  • NM_001406887.1:c.1714T>A
  • NM_001406888.1:c.1714T>A
  • NM_001406889.1:c.1714T>A
  • NM_001406890.1:c.1714T>A
  • NM_001406891.1:c.1714T>A
  • NM_001406892.1:c.1714T>A
  • NM_001406893.1:c.1714T>A
  • NM_001406894.1:c.1714T>A
  • NM_001406895.1:c.1714T>A
  • NM_001406896.1:c.1714T>A
  • NM_001406897.1:c.1714T>A
  • NM_001406898.1:c.1714T>A
  • NM_001406899.1:c.1714T>A
  • NM_001406900.1:c.1654T>A
  • NM_001406901.1:c.1645T>A
  • NM_001406902.1:c.1645T>A
  • NM_001406903.1:c.1688+3880T>A
  • NM_001406904.1:c.1606T>A
  • NM_001406905.1:c.1606T>A
  • NM_001406906.1:c.1558T>A
  • NM_001406907.1:c.1558T>A
  • NM_001406908.1:c.1601+3880T>A
  • NM_001406909.1:c.1546T>A
  • NM_001406910.1:c.1601+3880T>A
  • NM_001406911.1:c.1348T>A
  • NM_001406912.1:c.916T>A
  • NP_000526.1:p.Tyr707Asn
  • NP_000526.2:p.Tyr707Asn
  • NP_001018050.1:p.Tyr572Asn
  • NP_001308932.1:p.Tyr572Asn
  • NP_001308933.1:p.Tyr572Asn
  • NP_001308934.1:p.Tyr572Asn
  • NP_001308935.1:p.Tyr655Asn
  • NP_001308936.1:p.Tyr601Asn
  • NP_001308937.1:p.Tyr601Asn
  • NP_001308938.1:p.Tyr572Asn
  • NP_001308939.1:p.Tyr520Asn
  • NP_001308940.1:p.Tyr396Asn
  • NP_001308941.1:p.Tyr396Asn
  • NP_001308942.1:p.Tyr516Asn
  • NP_001308943.1:p.Tyr707Asn
  • NP_001308944.1:p.Tyr604Asn
  • NP_001393795.1:p.Tyr769Asn
  • NP_001393797.1:p.Tyr715Asn
  • NP_001393798.1:p.Tyr671Asn
  • NP_001393799.1:p.Tyr655Asn
  • NP_001393800.1:p.Tyr707Asn
  • NP_001393802.1:p.Tyr641Asn
  • NP_001393803.1:p.Tyr651Asn
  • NP_001393804.1:p.Tyr604Asn
  • NP_001393805.1:p.Tyr601Asn
  • NP_001393806.1:p.Tyr604Asn
  • NP_001393807.1:p.Tyr604Asn
  • NP_001393808.1:p.Tyr604Asn
  • NP_001393809.1:p.Tyr604Asn
  • NP_001393810.1:p.Tyr604Asn
  • NP_001393811.1:p.Tyr604Asn
  • NP_001393812.1:p.Tyr601Asn
  • NP_001393813.1:p.Tyr599Asn
  • NP_001393814.1:p.Tyr595Asn
  • NP_001393815.1:p.Tyr585Asn
  • NP_001393816.1:p.Tyr572Asn
  • NP_001393817.1:p.Tyr572Asn
  • NP_001393818.1:p.Tyr572Asn
  • NP_001393819.1:p.Tyr572Asn
  • NP_001393820.1:p.Tyr572Asn
  • NP_001393821.1:p.Tyr572Asn
  • NP_001393822.1:p.Tyr572Asn
  • NP_001393823.1:p.Tyr572Asn
  • NP_001393824.1:p.Tyr572Asn
  • NP_001393825.1:p.Tyr572Asn
  • NP_001393826.1:p.Tyr572Asn
  • NP_001393827.1:p.Tyr572Asn
  • NP_001393828.1:p.Tyr572Asn
  • NP_001393829.1:p.Tyr552Asn
  • NP_001393830.1:p.Tyr549Asn
  • NP_001393831.1:p.Tyr549Asn
  • NP_001393833.1:p.Tyr536Asn
  • NP_001393834.1:p.Tyr536Asn
  • NP_001393835.1:p.Tyr520Asn
  • NP_001393836.1:p.Tyr520Asn
  • NP_001393838.1:p.Tyr516Asn
  • NP_001393840.1:p.Tyr450Asn
  • NP_001393841.1:p.Tyr306Asn
  • LRG_161t1:c.2119T>A
  • LRG_161:g.31228T>A
  • LRG_161p1:p.Tyr707Asn
  • NC_000007.13:g.6022510A>T
  • NM_000535.5:c.2119T>A
  • NR_003085.2:n.2201T>A
  • NR_136154.1:n.2206T>A
Protein change:
Y306N
Molecular consequence:
  • NM_001406872.1:c.2006+3880T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406903.1:c.1688+3880T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406908.1:c.1601+3880T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406910.1:c.1601+3880T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.2119T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001018040.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1963T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1801T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1801T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1558T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.1186T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.1186T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1546T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.2119T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406866.1:c.2305T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406868.1:c.2143T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406869.1:c.2011T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406870.1:c.1963T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406871.1:c.2119T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406873.1:c.1921T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406874.1:c.1951T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406875.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406876.1:c.1801T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406877.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406878.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406879.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406880.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406881.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406882.1:c.1810T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406883.1:c.1801T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406884.1:c.1795T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406885.1:c.1783T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406886.1:c.1753T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406887.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406888.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406889.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406890.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406891.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406892.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406893.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406894.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406895.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406896.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406897.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406898.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406899.1:c.1714T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406900.1:c.1654T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406901.1:c.1645T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406902.1:c.1645T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406904.1:c.1606T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406905.1:c.1606T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406906.1:c.1558T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406907.1:c.1558T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406909.1:c.1546T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406911.1:c.1348T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406912.1:c.916T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2206T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005036062Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Dec 18, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Predictive functional assay-based classification of PMS2 variants in Lynch syndrome.

Rayner E, Tiersma Y, Fortuno C, van Hees-Stuivenberg S, Drost M, Thompson B, Spurdle AB, de Wind N.

Hum Mutat. 2022 Sep;43(9):1249-1258. doi: 10.1002/humu.24387. Epub 2022 Apr 28.

PubMed [citation]
PMID:
35451539
PMCID:
PMC9545740

Details of each submission

From Ambry Genetics, SCV005036062.1

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

Description

The p.Y707N variant (also known as c.2119T>A), located in coding exon 12 of the PMS2 gene, results from a T to A substitution at nucleotide position 2119. The tyrosine at codon 707 is replaced by asparagine, an amino acid with dissimilar properties. In an assay testing PMS2 function, this variant showed a functionally abnormal result (Rayner E et al. Hum Mutat, 2022 Sep;43:1249-1258). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: May 7, 2024