ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.4025A>T (p.Gln1342Leu)
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_000548.5(TSC2):c.4025A>T (p.Gln1342Leu)
Variation ID: 1737138 Accession: VCV001737138.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16p13.3 16: 2084247 (GRCh38) [ NCBI UCSC ] 16: 2134248 (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 May 4, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000548.5:c.4025A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Gln1342Leu missense NM_001077183.3:c.3824A>T NP_001070651.1:p.Gln1275Leu missense NM_001114382.3:c.3956A>T NP_001107854.1:p.Gln1319Leu missense NM_001318827.2:c.3716A>T NP_001305756.1:p.Gln1239Leu missense NM_001318829.2:c.3680A>T NP_001305758.1:p.Gln1227Leu missense NM_001318831.2:c.3293A>T NP_001305760.1:p.Gln1098Leu missense NM_001318832.2:c.3857A>T NP_001305761.1:p.Gln1286Leu missense NM_001363528.2:c.3827A>T NP_001350457.1:p.Gln1276Leu missense NM_001370404.1:c.3893A>T NP_001357333.1:p.Gln1298Leu missense NM_001370405.1:c.3896A>T NP_001357334.1:p.Gln1299Leu missense NM_001406663.1:c.4022A>T NP_001393592.1:p.Gln1341Leu missense NM_001406664.1:c.3953A>T NP_001393593.1:p.Gln1318Leu missense NM_001406665.1:c.3947A>T NP_001393594.1:p.Gln1316Leu missense NM_001406667.1:c.3917A>T NP_001393596.1:p.Gln1306Leu missense NM_001406668.1:c.3914A>T NP_001393597.1:p.Gln1305Leu missense NM_001406670.1:c.3845A>T NP_001393599.1:p.Gln1282Leu missense NM_001406671.1:c.3815A>T NP_001393600.1:p.Gln1272Leu missense NM_001406673.1:c.3812A>T NP_001393602.1:p.Gln1271Leu missense NM_001406675.1:c.3809A>T NP_001393604.1:p.Gln1270Leu missense NM_001406676.1:c.3806A>T NP_001393605.1:p.Gln1269Leu missense NM_001406677.1:c.3767A>T NP_001393606.1:p.Gln1256Leu missense NM_001406678.1:c.3713A>T NP_001393607.1:p.Gln1238Leu missense NM_001406679.1:c.3677A>T NP_001393608.1:p.Gln1226Leu missense NM_001406680.1:c.3425A>T NP_001393609.1:p.Gln1142Leu missense NM_001406681.1:c.3365A>T NP_001393610.1:p.Gln1122Leu missense NM_001406682.1:c.3356A>T NP_001393611.1:p.Gln1119Leu missense NM_001406683.1:c.3356A>T NP_001393612.1:p.Gln1119Leu missense NM_001406684.1:c.3353A>T NP_001393613.1:p.Gln1118Leu missense NM_001406685.1:c.3227A>T NP_001393614.1:p.Gln1076Leu missense NM_001406686.1:c.3227A>T NP_001393615.1:p.Gln1076Leu missense NM_001406687.1:c.3224A>T NP_001393616.1:p.Gln1075Leu missense NM_001406688.1:c.3224A>T NP_001393617.1:p.Gln1075Leu missense NM_001406689.1:c.2612A>T NP_001393618.1:p.Gln871Leu missense NM_001406690.1:c.2552A>T NP_001393619.1:p.Gln851Leu missense NM_001406691.1:c.2549A>T NP_001393620.1:p.Gln850Leu missense NM_001406692.1:c.2483A>T NP_001393621.1:p.Gln828Leu missense NM_001406693.1:c.2483A>T NP_001393622.1:p.Gln828Leu missense NM_001406694.1:c.2483A>T NP_001393623.1:p.Gln828Leu missense NM_001406695.1:c.2480A>T NP_001393624.1:p.Gln827Leu missense NM_001406696.1:c.2480A>T NP_001393625.1:p.Gln827Leu missense NM_001406697.1:c.2480A>T NP_001393626.1:p.Gln827Leu missense NM_001406698.1:c.2222A>T NP_001393627.1:p.Gln741Leu missense NM_021055.3:c.3896A>T NP_066399.2:p.Gln1299Leu missense NR_176225.1:n.3977A>T NR_176226.1:n.4225A>T NR_176227.1:n.4153A>T NR_176228.1:n.3974A>T NR_176229.1:n.3934A>T NC_000016.10:g.2084247A>T NC_000016.9:g.2134248A>T NG_005895.1:g.39942A>T LRG_487:g.39942A>T LRG_487t1:c.4025A>T LRG_487p1:p.Gln1342Leu - Protein change
- Q1238L, Q1239L, Q1271L, Q1286L, Q1298L, Q1299L, Q828L, Q850L, Q1118L, Q1256L, Q1269L, Q1282L, Q1318L, Q1341L, Q827L, Q851L, Q871L, Q1075L, Q1076L, Q1098L, Q1122L, Q1226L, Q1270L, Q1275L, Q1276L, Q1316L, Q741L, Q1119L, Q1142L, Q1227L, Q1272L, Q1305L, Q1306L, Q1319L, Q1342L
- Other names
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- Canonical SPDI
- NC_000016.10:2084246:A: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
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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
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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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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TSC2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
10658 | 10852 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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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Uncertain significance (1) |
criteria provided, single submitter
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May 4, 2022 | RCV002359509.2 |
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
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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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Uncertain significance
(May 04, 2022)
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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: SCV002619672.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.Q1342L variant (also known as c.4025A>T), located in coding exon 33 of the TSC2 gene, results from an A to T substitution at nucleotide … (more)
The p.Q1342L variant (also known as c.4025A>T), located in coding exon 33 of the TSC2 gene, results from an A to T substitution at nucleotide position 4025. The glutamine at codon 1342 is replaced by leucine, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (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 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.