The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (3Cnet: 0.87). However, the evidence of pathogenicity is insufficient at this time.Therefore, this variant is classified as VUS according to the recommendation of ACMG/AMP guideline.
ClinVar Genomic variation as it relates to human health
NM_001018005.2(TPM1):c.85A>C (p.Lys29Gln)
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_001018005.2(TPM1):c.85A>C (p.Lys29Gln)
Variation ID: 2444273 Accession: VCV002444273.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 15q22.2 15: 63042914 (GRCh38) [ NCBI UCSC ] 15: 63335113 (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 Mar 18, 2023 Mar 18, 2023 Feb 23, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001018005.2:c.85A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001018005.1:p.Lys29Gln missense NM_000366.6:c.85A>C NP_000357.3:p.Lys29Gln missense NM_001018004.2:c.85A>C NP_001018004.1:p.Lys29Gln missense NM_001018006.2:c.85A>C NP_001018006.1:p.Lys29Gln missense NM_001018007.2:c.85A>C NP_001018007.1:p.Lys29Gln missense NM_001018020.2:c.85A>C NP_001018020.1:p.Lys29Gln missense NM_001301244.2:c.85A>C NP_001288173.1:p.Lys29Gln missense NM_001365776.1:c.85A>C NP_001352705.1:p.Lys29Gln missense NM_001365777.1:c.85A>C NP_001352706.1:p.Lys29Gln missense NM_001365778.1:c.85A>C NP_001352707.1:p.Lys29Gln missense NM_001365779.1:c.85A>C NP_001352708.1:p.Lys29Gln missense NM_001407322.1:c.85A>C NP_001394251.1:p.Lys29Gln missense NM_001407323.1:c.85A>C NP_001394252.1:p.Lys29Gln missense NM_001407324.1:c.85A>C NP_001394253.1:p.Lys29Gln missense NM_001407325.1:c.85A>C NP_001394254.1:p.Lys29Gln missense NM_001407326.1:c.85A>C NP_001394255.1:p.Lys29Gln missense NM_001407327.1:c.85A>C NP_001394256.1:p.Lys29Gln missense NM_001407328.1:c.85A>C NP_001394257.1:p.Lys29Gln missense NM_001407329.1:c.85A>C NP_001394258.1:p.Lys29Gln missense NM_001407330.1:c.85A>C NP_001394259.1:p.Lys29Gln missense NM_001407331.1:c.85A>C NP_001394260.1:p.Lys29Gln missense NM_001407332.1:c.85A>C NP_001394261.1:p.Lys29Gln missense NM_001407333.1:c.85A>C NP_001394262.1:p.Lys29Gln missense NM_001407334.1:c.85A>C NP_001394263.1:p.Lys29Gln missense NM_001407335.1:c.85A>C NP_001394264.1:p.Lys29Gln missense NM_001407336.1:c.85A>C NP_001394265.1:p.Lys29Gln missense NM_001407337.1:c.85A>C NP_001394266.1:p.Lys29Gln missense NM_001407338.1:c.85A>C NP_001394267.1:p.Lys29Gln missense NR_176337.1:n.168A>C NR_176338.1:n.168A>C NR_176339.1:n.168A>C NR_176340.1:n.168A>C NR_176341.1:n.168A>C NR_176342.1:n.168A>C NR_176343.1:n.168A>C NR_176344.1:n.168A>C NR_176345.1:n.168A>C NR_176346.1:n.168A>C NR_176347.1:n.168A>C NC_000015.10:g.63042914A>C NC_000015.9:g.63335113A>C NG_007557.1:g.5276A>C LRG_387:g.5276A>C LRG_387t1:c.85A>C LRG_387p1:p.Lys29Gln - Protein change
- K29Q
- Other names
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- Canonical SPDI
- NC_000015.10:63042913:A:C
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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. |
|||
| TPM1 | No evidence available | No evidence available |
GRCh38 GRCh37 |
854 | 902 | |
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
|
Feb 23, 2023 | RCV003153071.1 |
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 23, 2023)
|
criteria provided, single submitter
Method: clinical testing
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Hypertrophic cardiomyopathy 3
Affected status: yes
Allele origin:
unknown
|
3billion
Accession: SCV003841833.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of … (more)
The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (3Cnet: 0.87). However, the evidence of pathogenicity is insufficient at this time.Therefore, this variant is classified as VUS according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Left ventricular hypertrophy (present) , Congestive heart failure (present)
|
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 variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (3Cnet: 0.87). However, the evidence of pathogenicity is insufficient at this time.Therefore, this variant is classified as VUS according to the recommendation of ACMG/AMP guideline.
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 Mar 26, 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.