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NM_000535.7(PMS2):c.2134C>T (p.Leu712=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Oct 21, 2022
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:
RCV002416221.9

Allele description [Variation Report for NM_000535.7(PMS2):c.2134C>T (p.Leu712=)]

NM_000535.7(PMS2):c.2134C>T (p.Leu712=)

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.2134C>T (p.Leu712=)
HGVS:
  • NC_000007.14:g.5982864G>A
  • NG_008466.1:g.31243C>T
  • NM_000535.7:c.2134C>TMANE SELECT
  • NM_001322003.2:c.1729C>T
  • NM_001322004.2:c.1729C>T
  • NM_001322005.2:c.1729C>T
  • NM_001322006.2:c.1978C>T
  • NM_001322007.2:c.1816C>T
  • NM_001322008.2:c.1816C>T
  • NM_001322009.2:c.1729C>T
  • NM_001322010.2:c.1573C>T
  • NM_001322011.2:c.1201C>T
  • NM_001322012.2:c.1201C>T
  • NM_001322013.2:c.1561C>T
  • NM_001322014.2:c.2134C>T
  • NM_001322015.2:c.1825C>T
  • NP_000526.2:p.Leu712=
  • NP_001308932.1:p.Leu577=
  • NP_001308933.1:p.Leu577=
  • NP_001308934.1:p.Leu577=
  • NP_001308935.1:p.Leu660=
  • NP_001308936.1:p.Leu606=
  • NP_001308937.1:p.Leu606=
  • NP_001308938.1:p.Leu577=
  • NP_001308939.1:p.Leu525=
  • NP_001308940.1:p.Leu401=
  • NP_001308941.1:p.Leu401=
  • NP_001308942.1:p.Leu521=
  • NP_001308943.1:p.Leu712=
  • NP_001308944.1:p.Leu609=
  • LRG_161t1:c.2134C>T
  • LRG_161:g.31243C>T
  • NC_000007.13:g.6022495G>A
  • NM_000535.5:c.2134C>T
  • NR_136154.1:n.2221C>T
Links:
dbSNP: rs1583298448
NCBI 1000 Genomes Browser:
rs1583298448
Molecular consequence:
  • NR_136154.1:n.2221C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.2134C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322003.2:c.1729C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322004.2:c.1729C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322005.2:c.1729C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322006.2:c.1978C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322007.2:c.1816C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322008.2:c.1816C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322009.2:c.1729C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322010.2:c.1573C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322011.2:c.1201C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322012.2:c.1201C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322013.2:c.1561C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322014.2:c.2134C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322015.2:c.1825C>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
SCV002730020Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Oct 21, 2022) 		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, SCV002730020.2

#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: Nov 3, 2024