ACMG Criteria: PM4, PM2_SUP
ClinVar Genomic variation as it relates to human health
NM_000368.5(TSC1):c.1308_1310del (p.His437del)
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_000368.5(TSC1):c.1308_1310del (p.His437del)
Variation ID: 3234028 Accession: VCV003234028.1
- Type and length
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Deletion, 3 bp
- Location
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Cytogenetic: 9q34.13 9: 132907324-132907326 (GRCh38) [ NCBI UCSC ] 9: 135782711-135782713 (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 12, 2024 May 12, 2024 Jun 2, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000368.5:c.1308_1310del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000359.1:p.His437del inframe deletion NM_001162426.2:c.1305_1307del NP_001155898.1:p.His436del inframe deletion NM_001162427.2:c.1155_1157del NP_001155899.1:p.His386del inframe deletion NM_001362177.2:c.945_947del NP_001349106.1:p.His316del inframe deletion NM_001406592.1:c.1308_1310del NP_001393521.1:p.His437del inframe deletion NM_001406593.1:c.1308_1310del NP_001393522.1:p.His437del inframe deletion NM_001406594.1:c.1308_1310del NP_001393523.1:p.His437del inframe deletion NM_001406595.1:c.1308_1310del NP_001393524.1:p.His437del inframe deletion NM_001406596.1:c.1308_1310del NP_001393525.1:p.His437del inframe deletion NM_001406597.1:c.1305_1307del NP_001393526.1:p.His436del inframe deletion NM_001406598.1:c.1305_1307del NP_001393527.1:p.His436del inframe deletion NM_001406599.1:c.1305_1307del NP_001393528.1:p.His436del inframe deletion NM_001406600.1:c.1305_1307del NP_001393529.1:p.His436del inframe deletion NM_001406601.1:c.1308_1310del NP_001393530.1:p.His437del inframe deletion NM_001406602.1:c.1308_1310del NP_001393531.1:p.His437del inframe deletion NM_001406603.1:c.1305_1307del NP_001393532.1:p.His436del inframe deletion NM_001406604.1:c.1305_1307del NP_001393533.1:p.His436del inframe deletion NM_001406605.1:c.1308_1310del NP_001393534.1:p.His437del inframe deletion NM_001406606.1:c.1308_1310del NP_001393535.1:p.His437del inframe deletion NM_001406607.1:c.1308_1310del NP_001393536.1:p.His437del inframe deletion NM_001406608.1:c.1305_1307del NP_001393537.1:p.His436del inframe deletion NM_001406609.1:c.1305_1307del NP_001393538.1:p.His436del inframe deletion NM_001406610.1:c.1155_1157del NP_001393539.1:p.His386del inframe deletion NM_001406611.1:c.1152_1154del NP_001393540.1:p.His385del inframe deletion NM_001406612.1:c.1152_1154del NP_001393541.1:p.His385del inframe deletion NM_001406613.1:c.1152_1154del NP_001393542.1:p.His385del inframe deletion NM_001406614.1:c.945_947del NP_001393543.1:p.His316del inframe deletion NM_001406615.1:c.945_947del NP_001393544.1:p.His316del inframe deletion NM_001406616.1:c.945_947del NP_001393545.1:p.His316del inframe deletion NM_001406617.1:c.945_947del NP_001393546.1:p.His316del inframe deletion NM_001406618.1:c.945_947del NP_001393547.1:p.His316del inframe deletion NM_001406619.1:c.945_947del NP_001393548.1:p.His316del inframe deletion NM_001406620.1:c.942_944del NP_001393549.1:p.His315del inframe deletion NM_001406621.1:c.942_944del NP_001393550.1:p.His315del inframe deletion NM_001406622.1:c.942_944del NP_001393551.1:p.His315del inframe deletion NM_001406623.1:c.942_944del NP_001393552.1:p.His315del inframe deletion NM_001406624.1:c.945_947del NP_001393553.1:p.His316del inframe deletion NM_001406625.1:c.942_944del NP_001393554.1:p.His315del inframe deletion NM_001406626.1:c.357_359del NP_001393555.1:p.His120del inframe deletion NM_001406627.1:c.354_356del NP_001393556.1:p.His119del inframe deletion NM_001406628.1:c.354_356del NP_001393557.1:p.His119del inframe deletion NM_001406629.1:c.255_257del NP_001393558.1:p.His86del inframe deletion NM_001406630.1:c.255_257del NP_001393559.1:p.His86del inframe deletion NR_176214.1:n.1525_1527del non-coding transcript variant NR_176215.1:n.1525_1527del non-coding transcript variant NR_176216.1:n.1392_1394del non-coding transcript variant NR_176217.1:n.1522_1524del non-coding transcript variant NR_176218.1:n.1525_1527del non-coding transcript variant NC_000009.12:g.132907326_132907328del NC_000009.11:g.135782713_135782715del NG_012386.1:g.42308_42310del LRG_486:g.42308_42310del LRG_486t1:c.1306_1308del LRG_486p1:p.His437del - Protein change
- H119del, H120del, H315del, H316del, H385del, H386del, H436del, H437del, H86del
- Other names
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- Canonical SPDI
- NC_000009.12:132907323:TGGTG:TG
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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 | ||
|---|---|---|---|---|---|---|
| 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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| TSC1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
4848 | 4906 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
|
Jun 2, 2023 | RCV004546872.2 |
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
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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|---|---|---|---|---|---|
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Uncertain significance
(Jun 02, 2023)
|
criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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MVZ Medizinische Genetik Mainz
Accession: SCV005040860.1
First in ClinVar: May 12, 2024 Last updated: May 12, 2024 |
Comment:
ACMG Criteria: PM4, PM2_SUP
Number of individuals with the variant: 1
Clinical Features:
Multicystic kidney dysplasia (present) , Renal cyst (present) , Renal dysplasia (present) , Polycystic kidney disease (present) , Nephrocalcinosis (present) , Cystic renal dysplasia (present) … (more)
Multicystic kidney dysplasia (present) , Renal cyst (present) , Renal dysplasia (present) , Polycystic kidney disease (present) , Nephrocalcinosis (present) , Cystic renal dysplasia (present) , Renal cortical cysts (present) , Atrial septal defect (present) , Multiple renal cysts (present) , Abnormal renal morphology (present) , Medullary nephrocalcinosis (present) (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:
ACMG Criteria: PM4, PM2_SUP
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 Jun 02, 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.