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NM_000535.7(PMS2):c.218G>A (p.Cys73Tyr) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 27, 2020
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:
RCV001821472.4

Allele description [Variation Report for NM_000535.7(PMS2):c.218G>A (p.Cys73Tyr)]

NM_000535.7(PMS2):c.218G>A (p.Cys73Tyr)

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.218G>A (p.Cys73Tyr)
HGVS:
  • NC_000007.14:g.6004004C>T
  • NG_008466.1:g.10103G>A
  • NM_000535.7:c.218G>AMANE SELECT
  • NM_001322003.2:c.-188G>A
  • NM_001322004.2:c.-188G>A
  • NM_001322005.2:c.-188G>A
  • NM_001322006.2:c.218G>A
  • NM_001322007.1:c.3G>A
  • NM_001322007.2:c.3G>A
  • NM_001322008.2:c.3G>A
  • NM_001322009.2:c.-188G>A
  • NM_001322010.2:c.-188G>A
  • NM_001322011.2:c.-667G>A
  • NM_001322012.2:c.-667G>A
  • NM_001322013.2:c.-188G>A
  • NM_001322014.2:c.218G>A
  • NM_001322015.2:c.-267G>A
  • NP_000526.2:p.Cys73Tyr
  • NP_001308935.1:p.Cys73Tyr
  • NP_001308936.1:p.Met1Ile
  • NP_001308937.1:p.Met1Ile
  • NP_001308943.1:p.Cys73Tyr
  • LRG_161t1:c.218G>A
  • LRG_161:g.10103G>A
  • NC_000007.13:g.6043635C>T
  • NM_000535.5:c.218G>A
  • NM_000535.7:c.218G>A
  • NR_136154.1:n.305G>A
Protein change:
C73Y
Links:
dbSNP: rs1326865470
NCBI 1000 Genomes Browser:
rs1326865470
Molecular consequence:
  • NM_001322003.2:c.-188G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-188G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-188G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-188G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322010.2:c.-188G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-667G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-667G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-188G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-267G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322007.2:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001322008.2:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_000535.7:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.305G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002067474Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 27, 2020) 		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 Genetic Services Laboratory, University of Chicago, SCV002067474.2

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

Description

DNA sequence analysis of the PMS2 gene demonstrated a sequence change, c.218G>A, in exon 3 that results in an amino acid change, p.Cys73Tyr. This sequence change has been described in the gnomaD database with a low population frequency of 0.00039% (dbSNP rs1326865470). The p.Cys73Tyr change affects a moderately conserved amino acid residue located in a domain of the PMS2 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Cys73Tyr substitution. This sequence change does not appear to have been previously reported in patients with PMS2-related disorders. Due to the lack of sufficient evidences, the clinical significance of the p.Cys73Tyr change remains unknown at this time.

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

Last Updated: Sep 29, 2024