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Relating variation to medicine
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NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser) AND not specified
- Germline classification:
- Benign (10 submissions)
- Last evaluated:
- Apr 16, 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)
no assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4)
no assertion criteria provided
- Record status:
- current
- Accession:
- RCV000079103.42
Allele description [Variation Report for NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser)]
NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser)
- Gene:
- PMS2:PMS1 hom*olog 2, mismatch repair system component [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 7p22.1
- Genomic location:
- Chr7: 5987357 (on Assembly GRCh38)
- Chr7: 6026988 (on Assembly GRCh37)
- Preferred name:
- NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser)
- HGVS:
- NC_000007.14:g.5987357G>A
- NG_008466.1:g.26750C>T
- NM_000535.7:c.1408C>TMANE SELECT
- NM_001322003.2:c.1003C>T
- NM_001322004.2:c.1003C>T
- NM_001322005.2:c.1003C>T
- NM_001322006.2:c.1252C>T
- NM_001322007.2:c.1090C>T
- NM_001322008.2:c.1090C>T
- NM_001322009.2:c.1003C>T
- NM_001322010.2:c.847C>T
- NM_001322011.2:c.475C>T
- NM_001322012.2:c.475C>T
- NM_001322013.2:c.835C>T
- NM_001322014.2:c.1408C>T
- NM_001322015.2:c.1099C>T
- NP_000526.2:p.Pro470Ser
- NP_001308932.1:p.Pro335Ser
- NP_001308933.1:p.Pro335Ser
- NP_001308934.1:p.Pro335Ser
- NP_001308935.1:p.Pro418Ser
- NP_001308936.1:p.Pro364Ser
- NP_001308937.1:p.Pro364Ser
- NP_001308938.1:p.Pro335Ser
- NP_001308939.1:p.Pro283Ser
- NP_001308940.1:p.Pro159Ser
- NP_001308941.1:p.Pro159Ser
- NP_001308942.1:p.Pro279Ser
- NP_001308943.1:p.Pro470Ser
- NP_001308944.1:p.Pro367Ser
- LRG_161t1:c.1408C>T
- LRG_161:g.26750C>T
- LRG_161p1:p.Pro470Ser
- NC_000007.13:g.6026988G>A
- NM_000535.5:c.1408C>T
- NM_000535.6:c.1408C>T
- NP_000526.1:p.Pro470Ser
- NR_136154.1:n.1495C>T
- P54278:p.Pro470Ser
- p.P470S
- Protein change:
- P159S
- Links:
- UniProtKB: P54278#VAR_016134; dbSNP: rs1805321
- NCBI 1000 Genomes Browser:
- rs1805321
- Molecular consequence:
- NM_000535.7:c.1408C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322003.2:c.1003C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322004.2:c.1003C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322005.2:c.1003C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322006.2:c.1252C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322007.2:c.1090C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322008.2:c.1090C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322009.2:c.1003C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322010.2:c.847C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322011.2:c.475C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322012.2:c.475C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322013.2:c.835C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322014.2:c.1408C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001322015.2:c.1099C>T - missense variant - [Sequence Ontology: SO:0001583]
- NR_136154.1:n.1495C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- Observations:
- 2
Condition(s)
- Synonyms:
- AllHighlyPenetrant
- Identifiers:
- MedGen: CN169374
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Assertion and evidence details
- Clinical assertions
- Evidence
Help
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000086042 | ITMI | no classification provided | not provided | germline | reference population | PubMed (1) |
SCV000110972 | Eurofins Ntd Llc (ga) | criteria provided, single submitter (EGL ClinVar v180209 classification definitions) | Benign (Apr 16, 2018) | germline | clinical testing | Citation Link, |
SCV000304717 | PreventionGenetics, part of Exact Sciences | criteria provided, single submitter (ACMG Guidelines, 2015) | Benign | germline | clinical testing | PubMed (1) |
SCV000691974 | Mayo Clinic Laboratories, Mayo Clinic | no assertion criteria provided | Benign | unknown | clinical testing | |
SCV000711441 | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | criteria provided, single submitter (LMM Criteria) | Benign (Apr 20, 2017) | germline | clinical testing | PubMed (1) |
SCV001744259 | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus | no assertion criteria provided | Benign | germline | clinical testing | |
SCV001906094 | Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus See additional submitters | no assertion criteria provided | Benign | germline | clinical testing | |
SCV001922389 | Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters | no assertion criteria provided | Benign | germline | clinical testing | |
SCV001951485 | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters | no assertion criteria provided | Benign | germline | clinical testing | |
SCV001971498 | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters | no assertion criteria provided | Benign | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | not provided | 2 | 2 | not provided | not provided | not provided | clinical testing |
not provided | germline | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | unknown | 101 | 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, SCV000086042.1
# | 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 | 0.32469999999999999 | not provided | not provided | |
2 | germline | unknown | 46 | not provided | discovery | not provided | 0.378 | not provided | not provided | |
3 | germline | unknown | 50 | not provided | discovery | not provided | 0.29349999999999998 | not provided | not provided | |
4 | germline | unknown | 62 | not provided | discovery | not provided | 0.34510000000000002 | not provided | not provided | |
5 | germline | unknown | 331 | not provided | discovery | not provided | 0.40649999999999997 | not provided | not provided | |
6 | germline | unknown | 118 | not provided | discovery | not provided | 0.39219999999999999 | not provided | not provided | |
7 | germline | unknown | 681 | not provided | discovery | not provided | 0.3846 | not provided | not provided |
From Eurofins Ntd Llc (ga), SCV000110972.8
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 101 | 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 | 101 | not provided | not provided | not provided |
From PreventionGenetics, part of Exact Sciences, SCV000304717.1
# | 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, SCV000691974.1
# | 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, SCV000711441.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 2 | not provided | not provided | clinical testing | PubMed (1) |
Description
p.Pro470Ser in Exon 11 of PMS2: This variant is not expected to have clinical si gnificance because it has been identified in 45% (4560/10152) of Ashkenazi Jewis h chromosomes and 41% (52732/126656) of European chromosomes by the Genome Aggre gation Database (GnomAD, http://gnomad.broadinstitute.org; dbSNP rs1805321).
# | 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 | 2 | not provided | 2 | not provided |
From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744259.3
# | 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 Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus, SCV001906094.1
# | 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, SCV001922389.1
# | 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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001951485.1
# | 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 DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001971498.1
# | 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: Jul 7, 2024
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