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NM_000535.7(PMS2):c.2T>A (p.Met1Lys) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 31, 2018
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:
RCV000763593.9

Allele description [Variation Report for NM_000535.7(PMS2):c.2T>A (p.Met1Lys)]

NM_000535.7(PMS2):c.2T>A (p.Met1Lys)

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.2T>A (p.Met1Lys)
Other names:
p.M1K:ATG>AAG
HGVS:
  • NC_000007.14:g.6009018A>T
  • NG_008466.1:g.5089T>A
  • NG_050738.1:g.4768A>T
  • NM_000535.7:c.2T>AMANE SELECT
  • NM_001322003.2:c.-399T>A
  • NM_001322004.2:c.-264T>A
  • NM_001322005.2:c.-594T>A
  • NM_001322006.2:c.2T>A
  • NM_001322007.2:c.-214T>A
  • NM_001322008.2:c.-74T>A
  • NM_001322009.2:c.-589T>A
  • NM_001322010.2:c.-264T>A
  • NM_001322011.2:c.-883T>A
  • NM_001322012.2:c.-878T>A
  • NM_001322013.2:c.-399T>A
  • NM_001322014.2:c.2T>A
  • NM_001322015.2:c.-478T>A
  • NP_000526.2:p.Met1Lys
  • NP_001308935.1:p.Met1Lys
  • NP_001308943.1:p.Met1Lys
  • LRG_161t1:c.2T>A
  • LRG_161:g.5089T>A
  • NC_000007.13:g.6048649A>T
  • NM_000535.5:c.2T>A
  • NM_000535.6:c.2T>A
  • NR_136154.1:n.89T>A
  • p.M1K
Protein change:
M1K
Links:
dbSNP: rs587780059
NCBI 1000 Genomes Browser:
rs587780059
Molecular consequence:
  • NM_001322003.2:c.-399T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-264T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-594T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322007.2:c.-214T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322008.2:c.-74T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-589T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322010.2:c.-264T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-883T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-878T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-399T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-478T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000535.7:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001322006.2:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001322014.2:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_000535.7:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.89T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Mismatch repair cancer syndrome 1 (MMRCS1)
Synonyms:
BRAIN TUMOR-POLYPOSIS SYNDROME 1; BTP1 SYNDROME; CHILDHOOD CANCER SYNDROME; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010159; MedGen: C5399763; Orphanet: 252202; OMIM: 276300
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
SCV000894432Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 31, 2018) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot 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
PMC

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.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]
PMCID:
PMC4544753
PMID:
25741868
DOI:
10.1038/gim.2015.30

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV000894432.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024