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NM_000535.7(PMS2):c.2143C>T (p.His715Tyr) AND Lynch syndrome 4

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 4, 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:
RCV001257484.1

Allele description [Variation Report for NM_000535.7(PMS2):c.2143C>T (p.His715Tyr)]

NM_000535.7(PMS2):c.2143C>T (p.His715Tyr)

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.2143C>T (p.His715Tyr)
HGVS:
  • NC_000007.14:g.5982855G>A
  • NG_008466.1:g.31252C>T
  • NM_000535.7:c.2143C>TMANE SELECT
  • NM_001322003.2:c.1738C>T
  • NM_001322004.2:c.1738C>T
  • NM_001322005.2:c.1738C>T
  • NM_001322006.2:c.1987C>T
  • NM_001322007.2:c.1825C>T
  • NM_001322008.2:c.1825C>T
  • NM_001322009.2:c.1738C>T
  • NM_001322010.2:c.1582C>T
  • NM_001322011.2:c.1210C>T
  • NM_001322012.2:c.1210C>T
  • NM_001322013.2:c.1570C>T
  • NM_001322014.2:c.2143C>T
  • NM_001322015.2:c.1834C>T
  • NP_000526.2:p.His715Tyr
  • NP_001308932.1:p.His580Tyr
  • NP_001308933.1:p.His580Tyr
  • NP_001308934.1:p.His580Tyr
  • NP_001308935.1:p.His663Tyr
  • NP_001308936.1:p.His609Tyr
  • NP_001308937.1:p.His609Tyr
  • NP_001308938.1:p.His580Tyr
  • NP_001308939.1:p.His528Tyr
  • NP_001308940.1:p.His404Tyr
  • NP_001308941.1:p.His404Tyr
  • NP_001308942.1:p.His524Tyr
  • NP_001308943.1:p.His715Tyr
  • NP_001308944.1:p.His612Tyr
  • LRG_161t1:c.2143C>T
  • LRG_161:g.31252C>T
  • NC_000007.13:g.6022486G>A
  • NM_000535.5:c.2143C>T
  • NR_136154.1:n.2230C>T
Protein change:
H404Y
Links:
dbSNP: rs747494931
NCBI 1000 Genomes Browser:
rs747494931
Molecular consequence:
  • NM_000535.7:c.2143C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1738C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1738C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1738C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1987C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1825C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1825C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1738C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1582C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.1210C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.1210C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1570C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.2143C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1834C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2230C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Lynch syndrome 4 (LYNCH4)
Synonyms:
Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:
MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001434293Division of Medical Genetics, University of Washington - CSER_CHARM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Oct 4, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Division of Medical Genetics, University of Washington - CSER_CHARM, SCV001434293.1

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

Description

To our knowledge, this sequence variant has not been previously reported in the literature. This variant is not present in population databases (https://gnomad.broadinstitute.org/). In silico analyses indicate this is an evolutionarily conserved residue. Thus, it is unknown at this time whether this variant increases cancer risk. PM2; PP3

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

Last Updated: Sep 29, 2024