The c.3493C>T (p.L1165F) alteration is located in exon 27 (coding exon 27) of the PLEKHA5 gene. This alteration results from a C to T substitution at nucleotide position 3493, causing the leucine (L) at amino acid position 1165 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_001256470.2(PLEKHA5):c.3817C>T (p.Leu1273Phe)
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)
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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_001256470.2(PLEKHA5):c.3817C>T (p.Leu1273Phe)
Variation ID: 3214788 Accession: VCV003214788.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 12p12.3 12: 19369755 (GRCh38) [ NCBI UCSC ] 12: 19522689 (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 8, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001256470.2:c.3817C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001243399.1:p.Leu1273Phe missense NM_001143821.3:c.3493C>T NP_001137293.2:p.Leu1165Phe missense NM_001190860.1:c.3265C>T NP_001177789.1:p.Leu1089Phe missense NM_001256787.2:c.3265C>T NP_001243716.1:p.Leu1089Phe missense NM_001385923.1:c.3799C>T NP_001372852.1:p.Leu1267Phe missense NM_001385924.1:c.3781C>T NP_001372853.1:p.Leu1261Phe missense NM_001385925.1:c.3763C>T NP_001372854.1:p.Leu1255Phe missense NM_001385926.1:c.3754+3646C>T intron variant NM_001385927.1:c.3697C>T NP_001372856.1:p.Leu1233Phe missense NM_001385928.1:c.3649C>T NP_001372857.1:p.Leu1217Phe missense NM_001385929.1:c.3628C>T NP_001372858.1:p.Leu1210Phe missense NM_001385930.1:c.3610C>T NP_001372859.1:p.Leu1204Phe missense NM_001385931.1:c.3592C>T NP_001372860.1:p.Leu1198Phe missense NM_001385932.1:c.3508C>T NP_001372861.1:p.Leu1170Phe missense NM_001385933.1:c.3493C>T NP_001372862.1:p.Leu1165Phe missense NM_001385934.1:c.3454C>T NP_001372863.1:p.Leu1152Phe missense NM_001385935.1:c.3439C>T NP_001372864.1:p.Leu1147Phe missense NM_001385936.1:c.3436C>T NP_001372865.1:p.Leu1146Phe missense NM_001385937.1:c.3397C>T NP_001372866.1:p.Leu1133Phe missense NM_001385938.1:c.3304C>T NP_001372867.1:p.Leu1102Phe missense NM_001385939.1:c.3304C>T NP_001372868.1:p.Leu1102Phe missense NM_001385940.1:c.3301C>T NP_001372869.1:p.Leu1101Phe missense NM_001385941.1:c.3286C>T NP_001372870.1:p.Leu1096Phe missense NM_001385942.1:c.3268C>T NP_001372871.1:p.Leu1090Phe missense NM_001385943.1:c.3256+3646C>T intron variant NM_001385944.1:c.3250C>T NP_001372873.1:p.Leu1084Phe missense NM_001385945.1:c.3238C>T NP_001372874.1:p.Leu1080Phe missense NM_001385946.1:c.3235C>T NP_001372875.1:p.Leu1079Phe missense NM_001385947.1:c.3223+3646C>T intron variant NM_001385948.1:c.3220C>T NP_001372877.1:p.Leu1074Phe missense NM_001385949.1:c.3217C>T NP_001372878.1:p.Leu1073Phe missense NM_001385950.1:c.3184C>T NP_001372879.1:p.Leu1062Phe missense NM_001385951.1:c.3115C>T NP_001372880.1:p.Leu1039Phe missense NM_001385952.1:c.3115C>T NP_001372881.1:p.Leu1039Phe missense NM_001385953.1:c.3112C>T NP_001372882.1:p.Leu1038Phe missense NM_001385954.1:c.3049C>T NP_001372883.1:p.Leu1017Phe missense NM_001385955.1:c.2995C>T NP_001372884.1:p.Leu999Phe missense NM_001385956.1:c.2995C>T NP_001372885.1:p.Leu999Phe missense NM_001385957.1:c.2995C>T NP_001372886.1:p.Leu999Phe missense NM_001385958.1:c.2980C>T NP_001372887.1:p.Leu994Phe missense NM_001385959.1:c.2932+3646C>T intron variant NM_001385960.1:c.2911C>T NP_001372889.1:p.Leu971Phe missense NM_001385961.1:c.2911C>T NP_001372890.1:p.Leu971Phe missense NM_001385962.1:c.2893C>T NP_001372891.1:p.Leu965Phe missense NM_001385963.1:c.2890C>T NP_001372892.1:p.Leu964Phe missense NM_001385964.1:c.2848+3646C>T intron variant NM_001385965.1:c.2848C>T NP_001372894.1:p.Leu950Phe missense NM_001385966.1:c.2845C>T NP_001372895.1:p.Leu949Phe missense NM_001385967.1:c.2824C>T NP_001372896.1:p.Leu942Phe missense NM_001385968.1:c.3493C>T NP_001372897.1:p.Leu1165Phe missense NM_001385969.1:c.2995C>T NP_001372898.1:p.Leu999Phe missense NM_001385970.1:c.2995C>T NP_001372899.1:p.Leu999Phe missense NM_001385971.1:c.2995C>T NP_001372900.1:p.Leu999Phe missense NM_001385972.1:c.2995C>T NP_001372901.1:p.Leu999Phe missense NM_001385973.1:c.2980C>T NP_001372902.1:p.Leu994Phe missense NM_019012.6:c.3319C>T NP_061885.2:p.Leu1107Phe missense NR_169816.1:n.3708C>T non-coding transcript variant NR_169817.1:n.3313C>T non-coding transcript variant NR_169818.1:n.3900C>T non-coding transcript variant NR_169819.1:n.3879C>T non-coding transcript variant NR_169820.1:n.4049C>T non-coding transcript variant NR_169821.1:n.3339C>T non-coding transcript variant NC_000012.12:g.19369755C>T NC_000012.11:g.19522689C>T - Protein change
- L1038F, L1080F, L1090F, L1107F, L1133F, L1146F, L1165F, L1198F, L1233F, L1273F, L971F, L1017F, L1062F, L1074F, L1084F, L1096F, L1102F, L1152F, L1217F, L1255F, L1261F, L1267F, L950F, L1039F, L1073F, L1089F, L1170F, L1210F, L942F, L949F, L964F, L999F, L1079F, L1101F, L1147F, L1204F, L965F, L994F
- Other names
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- Canonical SPDI
- NC_000012.12:19369754:C: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 | ||
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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
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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| 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
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. |
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| Uncertain significance (1) |
criteria provided, single submitter
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Jan 8, 2024 | RCV004514139.1 |
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
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
(Jan 08, 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: SCV005004794.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.3493C>T (p.L1165F) alteration is located in exon 27 (coding exon 27) of the PLEKHA5 gene. This alteration results from a C to T substitution … (more)
The c.3493C>T (p.L1165F) alteration is located in exon 27 (coding exon 27) of the PLEKHA5 gene. This alteration results from a C to T substitution at nucleotide position 3493, causing the leucine (L) at amino acid position 1165 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, 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 c.3493C>T (p.L1165F) alteration is located in exon 27 (coding exon 27) of the PLEKHA5 gene. This alteration results from a C to T substitution at nucleotide position 3493, causing the leucine (L) at amino acid position 1165 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, 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 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.