NM_000535.7(PMS2):c.1454C>A (p.Thr485Lys) AND not specified

Germline classification:: Benign (7 submissions)
Last evaluated:: Mar 21, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000079104.35

Allele description [Variation Report for NM_000535.7(PMS2):c.1454C>A (p.Thr485Lys)]

NM_000535.7(PMS2):c.1454C>A (p.Thr485Lys)

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.1454C>A (p.Thr485Lys)

HGVS:

NC_000007.14:g.5987311G>T
NG_008466.1:g.26796C>A
NM_000535.7:c.1454C>AMANE SELECT
NM_001322003.2:c.1049C>A
NM_001322004.2:c.1049C>A
NM_001322005.2:c.1049C>A
NM_001322006.2:c.1298C>A
NM_001322007.2:c.1136C>A
NM_001322008.2:c.1136C>A
NM_001322009.2:c.1049C>A
NM_001322010.2:c.893C>A
NM_001322011.2:c.521C>A
NM_001322012.2:c.521C>A
NM_001322013.2:c.881C>A
NM_001322014.2:c.1454C>A
NM_001322015.2:c.1145C>A
NP_000526.2:p.Thr485Lys
NP_001308932.1:p.Thr350Lys
NP_001308933.1:p.Thr350Lys
NP_001308934.1:p.Thr350Lys
NP_001308935.1:p.Thr433Lys
NP_001308936.1:p.Thr379Lys
NP_001308937.1:p.Thr379Lys
NP_001308938.1:p.Thr350Lys
NP_001308939.1:p.Thr298Lys
NP_001308940.1:p.Thr174Lys
NP_001308941.1:p.Thr174Lys
NP_001308942.1:p.Thr294Lys
NP_001308943.1:p.Thr485Lys
NP_001308944.1:p.Thr382Lys
LRG_161t1:c.1454C>A
LRG_161:g.26796C>A
LRG_161p1:p.Thr485Lys
NC_000007.13:g.6026942G>T
NM_000535.5:c.1454C>A
NM_000535.6:c.1454C>A
NP_000526.1:p.Thr485Lys
NR_136154.1:n.1541C>A
P54278:p.Thr485Lys
p.T485K

Protein change:

T174K

Links:

UniProtKB: P54278#VAR_012970; dbSNP: rs1805323

NCBI 1000 Genomes Browser:

rs1805323

Molecular consequence:

NM_000535.7:c.1454C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1049C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1049C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1049C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1298C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1136C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1136C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1049C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.893C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.521C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.521C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.881C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1454C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1145C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.1541C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000086044	ITMI	no classification provided	not provided	germline	reference population	PubMed (1) [See all records that cite this PMID]
SCV000110973	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Benign (Mar 21, 2018)	germline	clinical testing	Citation Link,
SCV000304719	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000691973	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign	unknown	clinical testing
SCV000711442	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Apr 20, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001906413	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001924426	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	14	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	3	3	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
African	germline	unknown	not provided	not provided	not provided	43	not provided	reference population
African_European	germline	unknown	not provided	not provided	not provided	46	not provided	reference population
Central_Asian	germline	unknown	not provided	not provided	not provided	50	not provided	reference population
East_Asian	germline	unknown	not provided	not provided	not provided	62	not provided	reference population
European	germline	unknown	not provided	not provided	not provided	331	not provided	reference population
Hispanic	germline	unknown	not provided	not provided	not provided	118	not provided	reference population
Whole_cohort	germline	unknown	not provided	not provided	not provided	681	not provided	reference population

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]

PMID:: 24728327
PMCID:: PMC3984285

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

See all PubMed Citations (3)

Details of each submission

From ITMI, SCV000086044.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	African	not provided	not provided	not provided	reference population	PubMed (1)
2	African_European	not provided	not provided	not provided	reference population	PubMed (1)
3	Central_Asian	not provided	not provided	not provided	reference population	PubMed (1)
4	East_Asian	not provided	not provided	not provided	reference population	PubMed (1)
5	European	not provided	not provided	not provided	reference population	PubMed (1)
6	Hispanic	not provided	not provided	not provided	reference population	PubMed (1)
7	Whole_cohort	not provided	not provided	not provided	reference population	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	43	not provided	discovery		not provided	0.0116	not provided	not provided
2	germline	unknown	46	not provided	discovery		not provided	0.0435	not provided	not provided
3	germline	unknown	50	not provided	discovery		not provided	0.12	not provided	not provided
4	germline	unknown	62	not provided	discovery		not provided	0.40870000000000001	not provided	not provided
5	germline	unknown	331	not provided	discovery		not provided	0.0425	not provided	not provided
6	germline	unknown	118	not provided	discovery		not provided	0.0212	not provided	not provided
7	germline	unknown	681	not provided	discovery		not provided	0.0764	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000110973.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	14	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		14	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000304719.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000691973.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000711442.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (1)

Description

p.Thr485Lys in exon 11 of PMS2: This variant is not expected to have clinical si gnificance because it has been identified in 35% (3077/8632) of East Asian chrom osomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org ; dbSNP rs1805323).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		3	not provided	3	not provided

From Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus, SCV001906413.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001924426.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 26, 2024

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