The c.3461C>T (p.S1154L) 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 3461, causing the serine (S) at amino acid position 1154 to be replaced by a leucine (L). 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.3785C>T (p.Ser1262Leu)
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_001256470.2(PLEKHA5):c.3785C>T (p.Ser1262Leu)
Variation ID: 3214787 Accession: VCV003214787.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 12p12.3 12: 19369723 (GRCh38) [ NCBI UCSC ] 12: 19522657 (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 Feb 14, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001256470.2:c.3785C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001243399.1:p.Ser1262Leu missense NM_001143821.3:c.3461C>T NP_001137293.2:p.Ser1154Leu missense NM_001190860.1:c.3233C>T NP_001177789.1:p.Ser1078Leu missense NM_001256787.2:c.3233C>T NP_001243716.1:p.Ser1078Leu missense NM_001385923.1:c.3767C>T NP_001372852.1:p.Ser1256Leu missense NM_001385924.1:c.3749C>T NP_001372853.1:p.Ser1250Leu missense NM_001385925.1:c.3731C>T NP_001372854.1:p.Ser1244Leu missense NM_001385926.1:c.3754+3614C>T intron variant NM_001385927.1:c.3665C>T NP_001372856.1:p.Ser1222Leu missense NM_001385928.1:c.3617C>T NP_001372857.1:p.Ser1206Leu missense NM_001385929.1:c.3596C>T NP_001372858.1:p.Ser1199Leu missense NM_001385930.1:c.3578C>T NP_001372859.1:p.Ser1193Leu missense NM_001385931.1:c.3560C>T NP_001372860.1:p.Ser1187Leu missense NM_001385932.1:c.3476C>T NP_001372861.1:p.Ser1159Leu missense NM_001385933.1:c.3461C>T NP_001372862.1:p.Ser1154Leu missense NM_001385934.1:c.3422C>T NP_001372863.1:p.Ser1141Leu missense NM_001385935.1:c.3407C>T NP_001372864.1:p.Ser1136Leu missense NM_001385936.1:c.3404C>T NP_001372865.1:p.Ser1135Leu missense NM_001385937.1:c.3365C>T NP_001372866.1:p.Ser1122Leu missense NM_001385938.1:c.3272C>T NP_001372867.1:p.Ser1091Leu missense NM_001385939.1:c.3272C>T NP_001372868.1:p.Ser1091Leu missense NM_001385940.1:c.3269C>T NP_001372869.1:p.Ser1090Leu missense NM_001385941.1:c.3254C>T NP_001372870.1:p.Ser1085Leu missense NM_001385942.1:c.3236C>T NP_001372871.1:p.Ser1079Leu missense NM_001385943.1:c.3256+3614C>T intron variant NM_001385944.1:c.3218C>T NP_001372873.1:p.Ser1073Leu missense NM_001385945.1:c.3206C>T NP_001372874.1:p.Ser1069Leu missense NM_001385946.1:c.3203C>T NP_001372875.1:p.Ser1068Leu missense NM_001385947.1:c.3223+3614C>T intron variant NM_001385948.1:c.3188C>T NP_001372877.1:p.Ser1063Leu missense NM_001385949.1:c.3185C>T NP_001372878.1:p.Ser1062Leu missense NM_001385950.1:c.3152C>T NP_001372879.1:p.Ser1051Leu missense NM_001385951.1:c.3083C>T NP_001372880.1:p.Ser1028Leu missense NM_001385952.1:c.3083C>T NP_001372881.1:p.Ser1028Leu missense NM_001385953.1:c.3080C>T NP_001372882.1:p.Ser1027Leu missense NM_001385954.1:c.3017C>T NP_001372883.1:p.Ser1006Leu missense NM_001385955.1:c.2963C>T NP_001372884.1:p.Ser988Leu missense NM_001385956.1:c.2963C>T NP_001372885.1:p.Ser988Leu missense NM_001385957.1:c.2963C>T NP_001372886.1:p.Ser988Leu missense NM_001385958.1:c.2948C>T NP_001372887.1:p.Ser983Leu missense NM_001385959.1:c.2932+3614C>T intron variant NM_001385960.1:c.2879C>T NP_001372889.1:p.Ser960Leu missense NM_001385961.1:c.2879C>T NP_001372890.1:p.Ser960Leu missense NM_001385962.1:c.2861C>T NP_001372891.1:p.Ser954Leu missense NM_001385963.1:c.2858C>T NP_001372892.1:p.Ser953Leu missense NM_001385964.1:c.2848+3614C>T intron variant NM_001385965.1:c.2816C>T NP_001372894.1:p.Ser939Leu missense NM_001385966.1:c.2813C>T NP_001372895.1:p.Ser938Leu missense NM_001385967.1:c.2792C>T NP_001372896.1:p.Ser931Leu missense NM_001385968.1:c.3461C>T NP_001372897.1:p.Ser1154Leu missense NM_001385969.1:c.2963C>T NP_001372898.1:p.Ser988Leu missense NM_001385970.1:c.2963C>T NP_001372899.1:p.Ser988Leu missense NM_001385971.1:c.2963C>T NP_001372900.1:p.Ser988Leu missense NM_001385972.1:c.2963C>T NP_001372901.1:p.Ser988Leu missense NM_001385973.1:c.2948C>T NP_001372902.1:p.Ser983Leu missense NM_019012.6:c.3287C>T NP_061885.2:p.Ser1096Leu missense NR_169816.1:n.3676C>T non-coding transcript variant NR_169817.1:n.3281C>T non-coding transcript variant NR_169818.1:n.3868C>T non-coding transcript variant NR_169819.1:n.3847C>T non-coding transcript variant NR_169820.1:n.4017C>T non-coding transcript variant NR_169821.1:n.3307C>T non-coding transcript variant NC_000012.12:g.19369723C>T NC_000012.11:g.19522657C>T - Protein change
- S1027L, S1069L, S1079L, S1090L, S1187L, S1199L, S1262L, S939L, S960L, S983L, S1028L, S1051L, S1062L, S1073L, S1135L, S1136L, S1141L, S1159L, S1222L, S938L, S988L, S1078L, S1091L, S1193L, S1250L, S1256L, S953L, S954L, S1006L, S1063L, S1068L, S1085L, S1096L, S1122L, S1154L, S1206L, S1244L, S931L
- Other names
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- Canonical SPDI
- NC_000012.12:19369722: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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Feb 14, 2024 | RCV004514138.1 |
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
(Feb 14, 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: SCV005004793.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.3461C>T (p.S1154L) 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.3461C>T (p.S1154L) 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 3461, causing the serine (S) at amino acid position 1154 to be replaced by a leucine (L). 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.3461C>T (p.S1154L) 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 3461, causing the serine (S) at amino acid position 1154 to be replaced by a leucine (L). 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.