The p.L684M variant (also known as c.2050C>A), located in coding exon 12 of the PMS2 gene, results from a C to A substitution at nucleotide position 2050. The leucine at codon 684 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.2050C>A (p.Leu684Met)
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(1)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000535.7(PMS2):c.2050C>A (p.Leu684Met)
Variation ID: 1785065 Accession: VCV001785065.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5982948 (GRCh38) [ NCBI UCSC ] 7: 6022579 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 29, 2022 May 1, 2024 Mar 7, 2017 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000535.7:c.2050C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Leu684Met missense NM_001018040.1:c.1645C>A NP_001018050.1:p.Leu549Met missense NM_001322003.2:c.1645C>A NP_001308932.1:p.Leu549Met missense NM_001322004.2:c.1645C>A NP_001308933.1:p.Leu549Met missense NM_001322005.2:c.1645C>A NP_001308934.1:p.Leu549Met missense NM_001322006.2:c.1894C>A NP_001308935.1:p.Leu632Met missense NM_001322007.2:c.1732C>A NP_001308936.1:p.Leu578Met missense NM_001322008.2:c.1732C>A NP_001308937.1:p.Leu578Met missense NM_001322009.2:c.1645C>A NP_001308938.1:p.Leu549Met missense NM_001322010.2:c.1489C>A NP_001308939.1:p.Leu497Met missense NM_001322011.2:c.1117C>A NP_001308940.1:p.Leu373Met missense NM_001322012.2:c.1117C>A NP_001308941.1:p.Leu373Met missense NM_001322013.2:c.1477C>A NP_001308942.1:p.Leu493Met missense NM_001322014.2:c.2050C>A NP_001308943.1:p.Leu684Met missense NM_001322015.2:c.1741C>A NP_001308944.1:p.Leu581Met missense NM_001406866.1:c.2236C>A NP_001393795.1:p.Leu746Met missense NM_001406868.1:c.2074C>A NP_001393797.1:p.Leu692Met missense NM_001406869.1:c.1942C>A NP_001393798.1:p.Leu648Met missense NM_001406870.1:c.1894C>A NP_001393799.1:p.Leu632Met missense NM_001406871.1:c.2050C>A NP_001393800.1:p.Leu684Met missense NM_001406873.1:c.1852C>A NP_001393802.1:p.Leu618Met missense NM_001406874.1:c.1882C>A NP_001393803.1:p.Leu628Met missense NM_001406875.1:c.1741C>A NP_001393804.1:p.Leu581Met missense NM_001406876.1:c.1732C>A NP_001393805.1:p.Leu578Met missense NM_001406877.1:c.1741C>A NP_001393806.1:p.Leu581Met missense NM_001406878.1:c.1741C>A NP_001393807.1:p.Leu581Met missense NM_001406879.1:c.1741C>A NP_001393808.1:p.Leu581Met missense NM_001406880.1:c.1741C>A NP_001393809.1:p.Leu581Met missense NM_001406881.1:c.1741C>A NP_001393810.1:p.Leu581Met missense NM_001406882.1:c.1741C>A NP_001393811.1:p.Leu581Met missense NM_001406883.1:c.1732C>A NP_001393812.1:p.Leu578Met missense NM_001406884.1:c.1726C>A NP_001393813.1:p.Leu576Met missense NM_001406885.1:c.1714C>A NP_001393814.1:p.Leu572Met missense NM_001406886.1:c.1684C>A NP_001393815.1:p.Leu562Met missense NM_001406887.1:c.1645C>A NP_001393816.1:p.Leu549Met missense NM_001406888.1:c.1645C>A NP_001393817.1:p.Leu549Met missense NM_001406889.1:c.1645C>A NP_001393818.1:p.Leu549Met missense NM_001406890.1:c.1645C>A NP_001393819.1:p.Leu549Met missense NM_001406891.1:c.1645C>A NP_001393820.1:p.Leu549Met missense NM_001406892.1:c.1645C>A NP_001393821.1:p.Leu549Met missense NM_001406893.1:c.1645C>A NP_001393822.1:p.Leu549Met missense NM_001406894.1:c.1645C>A NP_001393823.1:p.Leu549Met missense NM_001406895.1:c.1645C>A NP_001393824.1:p.Leu549Met missense NM_001406896.1:c.1645C>A NP_001393825.1:p.Leu549Met missense NM_001406897.1:c.1645C>A NP_001393826.1:p.Leu549Met missense NM_001406898.1:c.1645C>A NP_001393827.1:p.Leu549Met missense NM_001406899.1:c.1645C>A NP_001393828.1:p.Leu549Met missense NM_001406900.1:c.1585C>A NP_001393829.1:p.Leu529Met missense NM_001406901.1:c.1576C>A NP_001393830.1:p.Leu526Met missense NM_001406902.1:c.1576C>A NP_001393831.1:p.Leu526Met missense NM_001406904.1:c.1537C>A NP_001393833.1:p.Leu513Met missense NM_001406905.1:c.1537C>A NP_001393834.1:p.Leu513Met missense NM_001406906.1:c.1489C>A NP_001393835.1:p.Leu497Met missense NM_001406907.1:c.1489C>A NP_001393836.1:p.Leu497Met missense NM_001406909.1:c.1477C>A NP_001393838.1:p.Leu493Met missense NM_001406911.1:c.1279C>A NP_001393840.1:p.Leu427Met missense NM_001406912.1:c.847C>A NP_001393841.1:p.Leu283Met missense NR_003085.2:n.2132C>A NR_136154.1:n.2137C>A non-coding transcript variant NC_000007.14:g.5982948G>T NC_000007.13:g.6022579G>T NG_008466.1:g.31159C>A LRG_161:g.31159C>A LRG_161t1:c.2050C>A LRG_161p1:p.Leu684Met - Protein change
- L427M, L618M, L648M, L373M, L493M, L513M, L549M, L628M, L684M, L692M, L746M, L283M, L526M, L562M, L572M, L578M, L581M, L632M, L497M, L529M, L576M
- Other names
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- Canonical SPDI
- NC_000007.14:5982947:G:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| PMS2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
5241 | 5343 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Mar 7, 2017 | RCV002421814.2 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Mar 07, 2017)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002728940.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.L684M variant (also known as c.2050C>A), located in coding exon 12 of the PMS2 gene, results from a C to A substitution at nucleotide … (more)
The p.L684M variant (also known as c.2050C>A), located in coding exon 12 of the PMS2 gene, results from a C to A substitution at nucleotide position 2050. The leucine at codon 684 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
|
Comment:
Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Comment:
The p.L684M variant (also known as c.2050C>A), located in coding exon 12 of the PMS2 gene, results from a C to A substitution at nucleotide position 2050. The leucine at codon 684 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated May 01, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.