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NM_000535.7(PMS2):c.2080_2081delinsAT (p.Asp694Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 11, 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:
RCV002422301.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2080_2081delinsAT (p.Asp694Ile)]

NM_000535.7(PMS2):c.2080_2081delinsAT (p.Asp694Ile)

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.2080_2081delinsAT (p.Asp694Ile)
HGVS:
  • NC_000007.14:g.5982917_5982918delinsAT
  • NG_008466.1:g.31189_31190delinsAT
  • NM_000535.7:c.2080_2081delinsATMANE SELECT
  • NM_001018040.1:c.1675_1676delGAinsAT
  • NM_001322003.2:c.1675_1676delinsAT
  • NM_001322004.2:c.1675_1676delinsAT
  • NM_001322005.2:c.1675_1676delinsAT
  • NM_001322006.2:c.1924_1925delinsAT
  • NM_001322007.2:c.1762_1763delinsAT
  • NM_001322008.2:c.1762_1763delinsAT
  • NM_001322009.2:c.1675_1676delinsAT
  • NM_001322010.2:c.1519_1520delinsAT
  • NM_001322011.2:c.1147_1148delinsAT
  • NM_001322012.2:c.1147_1148delinsAT
  • NM_001322013.2:c.1507_1508delinsAT
  • NM_001322014.2:c.2080_2081delinsAT
  • NM_001322015.2:c.1771_1772delinsAT
  • NM_001406866.1:c.2266_2267delGAinsAT
  • NM_001406868.1:c.2104_2105delGAinsAT
  • NM_001406869.1:c.1972_1973delGAinsAT
  • NM_001406870.1:c.1924_1925delGAinsAT
  • NM_001406871.1:c.2080_2081delGAinsAT
  • NM_001406873.1:c.1882_1883delGAinsAT
  • NM_001406874.1:c.1912_1913delGAinsAT
  • NM_001406875.1:c.1771_1772delGAinsAT
  • NM_001406876.1:c.1762_1763delGAinsAT
  • NM_001406877.1:c.1771_1772delGAinsAT
  • NM_001406878.1:c.1771_1772delGAinsAT
  • NM_001406879.1:c.1771_1772delGAinsAT
  • NM_001406880.1:c.1771_1772delGAinsAT
  • NM_001406881.1:c.1771_1772delGAinsAT
  • NM_001406882.1:c.1771_1772delGAinsAT
  • NM_001406883.1:c.1762_1763delGAinsAT
  • NM_001406884.1:c.1756_1757delGAinsAT
  • NM_001406885.1:c.1744_1745delGAinsAT
  • NM_001406886.1:c.1714_1715delGAinsAT
  • NM_001406887.1:c.1675_1676delGAinsAT
  • NM_001406888.1:c.1675_1676delGAinsAT
  • NM_001406889.1:c.1675_1676delGAinsAT
  • NM_001406890.1:c.1675_1676delGAinsAT
  • NM_001406891.1:c.1675_1676delGAinsAT
  • NM_001406892.1:c.1675_1676delGAinsAT
  • NM_001406893.1:c.1675_1676delGAinsAT
  • NM_001406894.1:c.1675_1676delGAinsAT
  • NM_001406895.1:c.1675_1676delGAinsAT
  • NM_001406896.1:c.1675_1676delGAinsAT
  • NM_001406897.1:c.1675_1676delGAinsAT
  • NM_001406898.1:c.1675_1676delGAinsAT
  • NM_001406899.1:c.1675_1676delGAinsAT
  • NM_001406900.1:c.1615_1616delGAinsAT
  • NM_001406901.1:c.1606_1607delGAinsAT
  • NM_001406902.1:c.1606_1607delGAinsAT
  • NM_001406904.1:c.1567_1568delGAinsAT
  • NM_001406905.1:c.1567_1568delGAinsAT
  • NM_001406906.1:c.1519_1520delGAinsAT
  • NM_001406907.1:c.1519_1520delGAinsAT
  • NM_001406909.1:c.1507_1508delGAinsAT
  • NM_001406911.1:c.1309_1310delGAinsAT
  • NM_001406912.1:c.877_878delGAinsAT
  • NP_000526.1:p.Asp694Ile
  • NP_000526.2:p.Asp694Ile
  • NP_001018050.1:p.Asp559Ile
  • NP_001308932.1:p.Asp559Ile
  • NP_001308933.1:p.Asp559Ile
  • NP_001308934.1:p.Asp559Ile
  • NP_001308935.1:p.Asp642Ile
  • NP_001308936.1:p.Asp588Ile
  • NP_001308937.1:p.Asp588Ile
  • NP_001308938.1:p.Asp559Ile
  • NP_001308939.1:p.Asp507Ile
  • NP_001308940.1:p.Asp383Ile
  • NP_001308941.1:p.Asp383Ile
  • NP_001308942.1:p.Asp503Ile
  • NP_001308943.1:p.Asp694Ile
  • NP_001308944.1:p.Asp591Ile
  • NP_001393795.1:p.Asp756Ile
  • NP_001393797.1:p.Asp702Ile
  • NP_001393798.1:p.Asp658Ile
  • NP_001393799.1:p.Asp642Ile
  • NP_001393800.1:p.Asp694Ile
  • NP_001393802.1:p.Asp628Ile
  • NP_001393803.1:p.Asp638Ile
  • NP_001393804.1:p.Asp591Ile
  • NP_001393805.1:p.Asp588Ile
  • NP_001393806.1:p.Asp591Ile
  • NP_001393807.1:p.Asp591Ile
  • NP_001393808.1:p.Asp591Ile
  • NP_001393809.1:p.Asp591Ile
  • NP_001393810.1:p.Asp591Ile
  • NP_001393811.1:p.Asp591Ile
  • NP_001393812.1:p.Asp588Ile
  • NP_001393813.1:p.Asp586Ile
  • NP_001393814.1:p.Asp582Ile
  • NP_001393815.1:p.Asp572Ile
  • NP_001393816.1:p.Asp559Ile
  • NP_001393817.1:p.Asp559Ile
  • NP_001393818.1:p.Asp559Ile
  • NP_001393819.1:p.Asp559Ile
  • NP_001393820.1:p.Asp559Ile
  • NP_001393821.1:p.Asp559Ile
  • NP_001393822.1:p.Asp559Ile
  • NP_001393823.1:p.Asp559Ile
  • NP_001393824.1:p.Asp559Ile
  • NP_001393825.1:p.Asp559Ile
  • NP_001393826.1:p.Asp559Ile
  • NP_001393827.1:p.Asp559Ile
  • NP_001393828.1:p.Asp559Ile
  • NP_001393829.1:p.Asp539Ile
  • NP_001393830.1:p.Asp536Ile
  • NP_001393831.1:p.Asp536Ile
  • NP_001393833.1:p.Asp523Ile
  • NP_001393834.1:p.Asp523Ile
  • NP_001393835.1:p.Asp507Ile
  • NP_001393836.1:p.Asp507Ile
  • NP_001393838.1:p.Asp503Ile
  • NP_001393840.1:p.Asp437Ile
  • NP_001393841.1:p.Asp293Ile
  • LRG_161t1:c.2080_2081delGAinsAT
  • LRG_161:g.31189_31190delinsAT
  • LRG_161p1:p.Asp694Ile
  • NC_000007.13:g.6022548_6022549delinsAT
  • NM_000535.5:c.2080_2081delGAinsAT
  • NR_003085.2:n.2162_2163delGAinsAT
  • NR_136154.1:n.2167_2168delinsAT
Protein change:
D293I
Molecular consequence:
  • NM_000535.7:c.2080_2081delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001018040.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1675_1676delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1675_1676delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1675_1676delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1924_1925delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1762_1763delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1762_1763delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1675_1676delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1519_1520delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.1147_1148delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.1147_1148delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1507_1508delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.2080_2081delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1771_1772delinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406866.1:c.2266_2267delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406868.1:c.2104_2105delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406869.1:c.1972_1973delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406870.1:c.1924_1925delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406871.1:c.2080_2081delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406873.1:c.1882_1883delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406874.1:c.1912_1913delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406875.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406876.1:c.1762_1763delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406877.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406878.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406879.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406880.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406881.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406882.1:c.1771_1772delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406883.1:c.1762_1763delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406884.1:c.1756_1757delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406885.1:c.1744_1745delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406886.1:c.1714_1715delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406887.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406888.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406889.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406890.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406891.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406892.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406893.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406894.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406895.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406896.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406897.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406898.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406899.1:c.1675_1676delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406900.1:c.1615_1616delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406901.1:c.1606_1607delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406902.1:c.1606_1607delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406904.1:c.1567_1568delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406905.1:c.1567_1568delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406906.1:c.1519_1520delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406907.1:c.1519_1520delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406909.1:c.1507_1508delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406911.1:c.1309_1310delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406912.1:c.877_878delGAinsAT - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2167_2168delinsAT - 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
SCV002725758Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Jul 11, 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, SCV002725758.2

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

Description

The c.2080_2081delGAinsAT variant (also known as p.D694I), located in coding exon 12 of the PMS2 gene, results from an in-frame deletion of GA and insertion of AT at nucleotide positions 2080 to 2081. This results in the substitution of the aspartic acid residue for an isoleucine residue at codon 694, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al., PLoS ONE 2012; 7(10):e46688). 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 1, 2024