ClinVar Genomic variation as it relates to human health
NM_000368.5(TSC1):c.2546_2552del (p.Asn849fs)
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_000368.5(TSC1):c.2546_2552del (p.Asn849fs)
Variation ID: 1792882 Accession: VCV001792882.1
- Type and length
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Deletion, 7 bp
- Location
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Cytogenetic: 9q34.13 9: 132900788-132900794 (GRCh38) [ NCBI UCSC ] 9: 135776175-135776181 (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 Nov 29, 2022 Jul 11, 2019 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000368.5:c.2546_2552del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000359.1:p.Asn849fs frameshift NM_000368.4:c.2546_2552delACAGGCA frameshift NM_001162426.2:c.2543_2549del NP_001155898.1:p.Asn848fs frameshift NM_001162427.2:c.2393_2399del NP_001155899.1:p.Asn798fs frameshift NM_001362177.2:c.2183_2189del NP_001349106.1:p.Asn728fs frameshift NM_001406592.1:c.2545_2551delAACAGGC NP_001393521.1:p.Asn849Serfs frameshift NM_001406593.1:c.2545_2551delAACAGGC NP_001393522.1:p.Asn849Serfs frameshift NM_001406594.1:c.2545_2551delAACAGGC NP_001393523.1:p.Asn849Serfs frameshift NM_001406595.1:c.2545_2551delAACAGGC NP_001393524.1:p.Asn849Serfs frameshift NM_001406596.1:c.2545_2551delAACAGGC NP_001393525.1:p.Asn849Serfs frameshift NM_001406597.1:c.2542_2548delAACAGGC NP_001393526.1:p.Asn848Serfs frameshift NM_001406598.1:c.2542_2548delAACAGGC NP_001393527.1:p.Asn848Serfs frameshift NM_001406599.1:c.2542_2548delAACAGGC NP_001393528.1:p.Asn848Serfs frameshift NM_001406600.1:c.2542_2548delAACAGGC NP_001393529.1:p.Asn848Serfs frameshift NM_001406601.1:c.2530_2536delAACAGGC NP_001393530.1:p.Asn844Serfs frameshift NM_001406602.1:c.2530_2536delAACAGGC NP_001393531.1:p.Asn844Serfs frameshift NM_001406603.1:c.2527_2533delAACAGGC NP_001393532.1:p.Asn843Serfs frameshift NM_001406604.1:c.2527_2533delAACAGGC NP_001393533.1:p.Asn843Serfs frameshift NM_001406605.1:c.2503_2509delAACAGGC NP_001393534.1:p.Asn835Serfs frameshift NM_001406606.1:c.2503_2509delAACAGGC NP_001393535.1:p.Asn835Serfs frameshift NM_001406607.1:c.2503_2509delAACAGGC NP_001393536.1:p.Asn835Serfs frameshift NM_001406608.1:c.2500_2506delAACAGGC NP_001393537.1:p.Asn834Serfs frameshift NM_001406609.1:c.2500_2506delAACAGGC NP_001393538.1:p.Asn834Serfs frameshift NM_001406610.1:c.2392_2398delAACAGGC NP_001393539.1:p.Asn798Serfs frameshift NM_001406611.1:c.2389_2395delAACAGGC NP_001393540.1:p.Asn797Serfs frameshift NM_001406612.1:c.2389_2395delAACAGGC NP_001393541.1:p.Asn797Serfs frameshift NM_001406613.1:c.2347_2353delAACAGGC NP_001393542.1:p.Asn783Serfs frameshift NM_001406614.1:c.2182_2188delAACAGGC NP_001393543.1:p.Asn728Serfs frameshift NM_001406615.1:c.2182_2188delAACAGGC NP_001393544.1:p.Asn728Serfs frameshift NM_001406616.1:c.2182_2188delAACAGGC NP_001393545.1:p.Asn728Serfs frameshift NM_001406617.1:c.2182_2188delAACAGGC NP_001393546.1:p.Asn728Serfs frameshift NM_001406618.1:c.2182_2188delAACAGGC NP_001393547.1:p.Asn728Serfs frameshift NM_001406619.1:c.2182_2188delAACAGGC NP_001393548.1:p.Asn728Serfs frameshift NM_001406620.1:c.2179_2185delAACAGGC NP_001393549.1:p.Asn727Serfs frameshift NM_001406621.1:c.2179_2185delAACAGGC NP_001393550.1:p.Asn727Serfs frameshift NM_001406622.1:c.2179_2185delAACAGGC NP_001393551.1:p.Asn727Serfs frameshift NM_001406623.1:c.2179_2185delAACAGGC NP_001393552.1:p.Asn727Serfs frameshift NM_001406624.1:c.2140_2146delAACAGGC NP_001393553.1:p.Asn714Serfs frameshift NM_001406625.1:c.2137_2143delAACAGGC NP_001393554.1:p.Asn713Serfs frameshift NM_001406626.1:c.1594_1600delAACAGGC NP_001393555.1:p.Asn532Serfs frameshift NM_001406627.1:c.1591_1597delAACAGGC NP_001393556.1:p.Asn531Serfs frameshift NM_001406628.1:c.1591_1597delAACAGGC NP_001393557.1:p.Asn531Serfs frameshift NM_001406629.1:c.1492_1498delAACAGGC NP_001393558.1:p.Asn498Serfs frameshift NM_001406630.1:c.1492_1498delAACAGGC NP_001393559.1:p.Asn498Serfs frameshift NR_176214.1:n.2595_2601delAACAGGC NR_176215.1:n.2762_2768delAACAGGC NR_176216.1:n.2629_2635delAACAGGC NR_176217.1:n.2759_2765delAACAGGC NR_176218.1:n.2758_2764delAACAGGC NC_000009.12:g.132900789_132900795del NC_000009.11:g.135776176_135776182del NG_012386.1:g.48840_48846del LRG_486:g.48840_48846del LRG_486t1:c.2545_2551del LRG_486p1:p.Asn849Serfs - Protein change
- N848fs, N728fs, N798fs, N849fs
- Other names
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- Canonical SPDI
- NC_000009.12:132900787:TGCCTGTT: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
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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TSC1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
4666 | 4715 |
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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Pathogenic (1) |
criteria provided, single submitter
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Jul 11, 2019 | RCV002433264.1 |
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
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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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Pathogenic
(Jul 11, 2019)
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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: SCV002740618.1
First in ClinVar: Nov 29, 2022 Last updated: Nov 29, 2022 |
Comment:
The c.2546_2552delACAGGCA pathogenic mutation, located in coding exon 18 of the TSC1 gene, results from a deletion of 7 nucleotides at nucleotide positions 2546 to … (more)
The c.2546_2552delACAGGCA pathogenic mutation, located in coding exon 18 of the TSC1 gene, results from a deletion of 7 nucleotides at nucleotide positions 2546 to 2552, causing a translational frameshift with a predicted alternate stop codon (p.N849Sfs*27). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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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 Dec 25, 2023
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.