NM_000535.7(PMS2):c.2033T>C (p.Ile678Thr) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 7, 2024
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:
RCV000131767.7

Allele description [Variation Report for NM_000535.7(PMS2):c.2033T>C (p.Ile678Thr)]

NM_000535.7(PMS2):c.2033T>C (p.Ile678Thr)

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.2033T>C (p.Ile678Thr)
HGVS:
  • NC_000007.14:g.5982965A>G
  • NG_008466.1:g.31142T>C
  • NM_000535.7:c.2033T>CMANE SELECT
  • NM_001322003.2:c.1628T>C
  • NM_001322004.2:c.1628T>C
  • NM_001322005.2:c.1628T>C
  • NM_001322006.2:c.1877T>C
  • NM_001322007.2:c.1715T>C
  • NM_001322008.2:c.1715T>C
  • NM_001322009.2:c.1628T>C
  • NM_001322010.2:c.1472T>C
  • NM_001322011.2:c.1100T>C
  • NM_001322012.2:c.1100T>C
  • NM_001322013.2:c.1460T>C
  • NM_001322014.2:c.2033T>C
  • NM_001322015.2:c.1724T>C
  • NP_000526.2:p.Ile678Thr
  • NP_001308932.1:p.Ile543Thr
  • NP_001308933.1:p.Ile543Thr
  • NP_001308934.1:p.Ile543Thr
  • NP_001308935.1:p.Ile626Thr
  • NP_001308936.1:p.Ile572Thr
  • NP_001308937.1:p.Ile572Thr
  • NP_001308938.1:p.Ile543Thr
  • NP_001308939.1:p.Ile491Thr
  • NP_001308940.1:p.Ile367Thr
  • NP_001308941.1:p.Ile367Thr
  • NP_001308942.1:p.Ile487Thr
  • NP_001308943.1:p.Ile678Thr
  • NP_001308944.1:p.Ile575Thr
  • LRG_161t1:c.2033T>C
  • LRG_161:g.31142T>C
  • NC_000007.13:g.6022596A>G
  • NM_000535.5:c.2033T>C
  • NM_000535.6:c.2033T>C
  • NR_136154.1:n.2120T>C
  • p.I678T
Protein change:
I367T
Links:
dbSNP: rs587782553
NCBI 1000 Genomes Browser:
rs587782553
Molecular consequence:
  • NM_000535.7:c.2033T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1628T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1628T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1628T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1877T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1715T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1715T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1628T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1472T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.1100T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.1100T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1460T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.2033T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1724T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2120T>C - 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000186813Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(May 7, 2024) 		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, SCV000186813.10

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

Description

The p.I678T variant (also known as c.2033T>C), located in coding exon 12 of the PMS2 gene, results from a T to C substitution at nucleotide position 2033. The isoleucine at codon 678 is replaced by threonine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear.

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

Last Updated: Sep 29, 2024