ClinVar Genomic variation as it relates to human health
NM_001256470.2(PLEKHA5):c.2660T>C (p.Ile887Thr)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001256470.2(PLEKHA5):c.2660T>C (p.Ile887Thr)
Variation ID: 3214785 Accession: VCV003214785.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 12p12.3 12: 19343432 (GRCh38) [ NCBI UCSC ] 12: 19496366 (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 May 1, 2024 May 1, 2024 Jan 29, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001256470.2:c.2660T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001243399.1:p.Ile887Thr missense NM_001143821.3:c.2525T>C NP_001137293.2:p.Ile842Thr missense NM_001190860.1:c.2108T>C NP_001177789.1:p.Ile703Thr missense NM_001256787.2:c.2108T>C NP_001243716.1:p.Ile703Thr missense NM_001385923.1:c.2642T>C NP_001372852.1:p.Ile881Thr missense NM_001385924.1:c.2624T>C NP_001372853.1:p.Ile875Thr missense NM_001385925.1:c.2606T>C NP_001372854.1:p.Ile869Thr missense NM_001385926.1:c.2660T>C NP_001372855.1:p.Ile887Thr missense NM_001385927.1:c.2540T>C NP_001372856.1:p.Ile847Thr missense NM_001385928.1:c.2492T>C NP_001372857.1:p.Ile831Thr missense NM_001385929.1:c.2660T>C NP_001372858.1:p.Ile887Thr missense NM_001385930.1:c.2642T>C NP_001372859.1:p.Ile881Thr missense NM_001385931.1:c.2624T>C NP_001372860.1:p.Ile875Thr missense NM_001385932.1:c.2351T>C NP_001372861.1:p.Ile784Thr missense NM_001385933.1:c.2336T>C NP_001372862.1:p.Ile779Thr missense NM_001385934.1:c.2486T>C NP_001372863.1:p.Ile829Thr missense NM_001385935.1:c.2282T>C NP_001372864.1:p.Ile761Thr missense NM_001385936.1:c.2468T>C NP_001372865.1:p.Ile823Thr missense NM_001385937.1:c.2429T>C NP_001372866.1:p.Ile810Thr missense NM_001385938.1:c.2338+13T>C intron variant NM_001385939.1:c.2336T>C NP_001372868.1:p.Ile779Thr missense NM_001385940.1:c.2144T>C NP_001372869.1:p.Ile715Thr missense NM_001385941.1:c.2318T>C NP_001372870.1:p.Ile773Thr missense NM_001385942.1:c.2300T>C NP_001372871.1:p.Ile767Thr missense NM_001385943.1:c.2351T>C NP_001372872.1:p.Ile784Thr missense NM_001385944.1:c.2282T>C NP_001372873.1:p.Ile761Thr missense NM_001385945.1:c.2081T>C NP_001372874.1:p.Ile694Thr missense NM_001385946.1:c.2267T>C NP_001372875.1:p.Ile756Thr missense NM_001385947.1:c.2318T>C NP_001372876.1:p.Ile773Thr missense NM_001385948.1:c.2254+13T>C intron variant NM_001385949.1:c.2249T>C NP_001372878.1:p.Ile750Thr missense NM_001385950.1:c.2027T>C NP_001372879.1:p.Ile676Thr missense NM_001385951.1:c.2147T>C NP_001372880.1:p.Ile716Thr missense NM_001385952.1:c.2147T>C NP_001372881.1:p.Ile716Thr missense NM_001385953.1:c.2144T>C NP_001372882.1:p.Ile715Thr missense NM_001385954.1:c.2081T>C NP_001372883.1:p.Ile694Thr missense NM_001385955.1:c.2027T>C NP_001372884.1:p.Ile676Thr missense NM_001385956.1:c.2027T>C NP_001372885.1:p.Ile676Thr missense NM_001385957.1:c.2027T>C NP_001372886.1:p.Ile676Thr missense NM_001385958.1:c.2014+13T>C intron variant NM_001385959.1:c.2027T>C NP_001372888.1:p.Ile676Thr missense NM_001385960.1:c.1943T>C NP_001372889.1:p.Ile648Thr missense NM_001385961.1:c.1943T>C NP_001372890.1:p.Ile648Thr missense NM_001385962.1:c.1925T>C NP_001372891.1:p.Ile642Thr missense NM_001385963.1:c.1922T>C NP_001372892.1:p.Ile641Thr missense NM_001385964.1:c.1943T>C NP_001372893.1:p.Ile648Thr missense NM_001385965.1:c.1880T>C NP_001372894.1:p.Ile627Thr missense NM_001385966.1:c.1877T>C NP_001372895.1:p.Ile626Thr missense NM_001385967.1:c.1856T>C NP_001372896.1:p.Ile619Thr missense NM_001385968.1:c.2525T>C NP_001372897.1:p.Ile842Thr missense NM_001385969.1:c.2027T>C NP_001372898.1:p.Ile676Thr missense NM_001385970.1:c.2027T>C NP_001372899.1:p.Ile676Thr missense NM_001385971.1:c.2027T>C NP_001372900.1:p.Ile676Thr missense NM_001385972.1:c.2027T>C NP_001372901.1:p.Ile676Thr missense NM_001385973.1:c.2014+13T>C intron variant NM_019012.6:c.2351T>C NP_061885.2:p.Ile784Thr missense NR_169816.1:n.2740T>C non-coding transcript variant NR_169817.1:n.2345T>C non-coding transcript variant NR_169818.1:n.2856T>C non-coding transcript variant NR_169819.1:n.2722T>C non-coding transcript variant NR_169820.1:n.2892T>C non-coding transcript variant NR_169821.1:n.2418T>C non-coding transcript variant NC_000012.12:g.19343432T>C NC_000012.11:g.19496366T>C - Protein change
- I619T, I648T, I676T, I756T, I767T, I847T, I875T, I887T, I626T, I716T, I761T, I869T, I881T, I642T, I694T, I703T, I773T, I842T, I627T, I641T, I715T, I750T, I779T, I784T, I810T, I823T, I829T, I831T
- Other names
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- Canonical SPDI
- NC_000012.12:19343431:T:C
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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
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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 | ||
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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
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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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PLEKHA5 | - | - |
GRCh38 GRCh37 |
88 | 125 |
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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Likely benign (1) |
criteria provided, single submitter
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Jan 29, 2024 | RCV004514136.1 |
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
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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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Likely benign
(Jan 29, 2024)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV005004791.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
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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. |
Citations for germline classification of this variant
HelpThere 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 Nov 03, 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.