This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ClinVar Genomic variation as it relates to human health
NM_015416.5(LETMD1):c.760G>A (p.Val254Met)
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.
Likely benign
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_015416.5(LETMD1):c.760G>A (p.Val254Met)
Variation ID: 2307447 Accession: VCV002307447.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 12q13.12 12: 51056243 (GRCh38) [ NCBI UCSC ] 12: 51450026 (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 Feb 8, 2023 May 1, 2024 Aug 16, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_015416.5:c.760G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_056231.3:p.Val254Met missense NM_001243689.2:c.799G>A NP_001230618.1:p.Val267Met missense NM_001300765.2:c.391-107G>A intron variant NM_001351312.2:c.592G>A NP_001338241.1:p.Val198Met missense NM_001351313.2:c.289G>A NP_001338242.1:p.Val97Met missense NM_001351315.2:c.781G>A NP_001338244.1:p.Val261Met missense NM_001351316.2:c.781G>A NP_001338245.1:p.Val261Met missense NM_001351317.2:c.760G>A NP_001338246.1:p.Val254Met missense NM_001351318.1:c.781G>A NP_001338247.1:p.Val261Met missense NM_001351319.2:c.592G>A NP_001338248.1:p.Val198Met missense NM_001351320.2:c.592G>A NP_001338249.1:p.Val198Met missense NM_001351321.2:c.490G>A NP_001338250.1:p.Val164Met missense NM_001351322.2:c.478G>A NP_001338251.1:p.Val160Met missense NM_001351323.2:c.478G>A NP_001338252.1:p.Val160Met missense NM_001351324.2:c.478G>A NP_001338253.1:p.Val160Met missense NM_001351325.2:c.457G>A NP_001338254.1:p.Val153Met missense NM_001351326.2:c.442G>A NP_001338255.1:p.Val148Met missense NM_001351327.2:c.442G>A NP_001338256.1:p.Val148Met missense NM_001351328.2:c.412-107G>A intron variant NM_001351330.2:c.409G>A NP_001338259.1:p.Val137Met missense NM_001351332.2:c.409G>A NP_001338261.1:p.Val137Met missense NM_001351333.2:c.391-107G>A intron variant NM_001351334.2:c.289G>A NP_001338263.1:p.Val97Met missense NM_001351335.2:c.289G>A NP_001338264.1:p.Val97Met missense NM_001351336.2:c.289G>A NP_001338265.1:p.Val97Met missense NM_001351337.2:c.391-107G>A intron variant NR_045017.1:n.693G>A NR_045018.1:n.702G>A NR_045019.2:n.591G>A non-coding transcript variant NR_147099.2:n.297G>A non-coding transcript variant NR_147100.2:n.1110G>A non-coding transcript variant NR_147101.2:n.959G>A non-coding transcript variant NR_147104.2:n.1146G>A non-coding transcript variant NR_147106.2:n.484G>A non-coding transcript variant NR_147107.2:n.1146G>A non-coding transcript variant NR_147108.2:n.707G>A non-coding transcript variant NR_147109.2:n.1193G>A non-coding transcript variant NR_147110.2:n.439G>A non-coding transcript variant NR_147111.2:n.252G>A non-coding transcript variant NR_147118.2:n.1311G>A non-coding transcript variant NR_147119.2:n.1345G>A non-coding transcript variant NC_000012.12:g.51056243G>A NC_000012.11:g.51450026G>A NG_029858.2:g.13024G>A NG_029858.3:g.13025G>A - Protein change
- V137M, V160M, V267M, V164M, V198M, V261M, V97M, V153M, V254M, V148M
- Other names
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- Canonical SPDI
- NC_000012.12:51056242:G:A
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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. |
|||
| LETMD1 | - | - |
GRCh38 GRCh37 |
29 | 66 | |
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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
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Aug 16, 2022 | RCV004149568.1 |
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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Likely benign
(Aug 16, 2022)
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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: SCV003636103.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (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:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
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 25, 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.