ClinVar Genomic variation as it relates to human health
NM_170707.4(LMNA):c.1616_1617delinsTT (p.Ala539Val)
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_170707.4(LMNA):c.1616_1617delinsTT (p.Ala539Val)
Variation ID: 3237189 Accession: VCV003237189.1
- Type and length
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Indel, 2 bp
- Location
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Cytogenetic: 1q22 1: 156137661-156137662 (GRCh38) [ NCBI UCSC ] 1: 156107452-156107453 (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 Jun 2, 2024 Jun 2, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_170707.4:c.1616_1617delinsTT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_733821.1:p.Ala539Val missense NM_005572.4:c.1616_1617delinsTT MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_005563.1:p.Ala539Val missense NM_001257374.3:c.1280_1281delinsTT NP_001244303.1:p.Ala427Val missense NM_001282624.2:c.1373_1374delinsTT NP_001269553.1:p.Ala458Val missense NM_001282625.2:c.1616_1617delinsTT NP_001269554.1:p.Ala539Val missense NM_001282626.2:c.1616_1617delinsTT NP_001269555.1:p.Ala539Val missense NM_001406983.1:c.1616_1617delinsTT NP_001393912.1:p.Ala539Val missense NM_001406984.1:c.1616_1617delinsTT NP_001393913.1:p.Ala539Val missense NM_001406985.1:c.1616_1617delinsTT NP_001393914.1:p.Ala539Val missense NM_001406986.1:c.1373_1374delinsTT NP_001393915.1:p.Ala458Val missense NM_001406987.1:c.1373_1374delinsTT NP_001393916.1:p.Ala458Val missense NM_001406988.1:c.1319_1320delinsTT NP_001393917.1:p.Ala440Val missense NM_001406989.1:c.1280_1281delinsTT NP_001393918.1:p.Ala427Val missense NM_001406990.1:c.1058_1059delinsTT NP_001393919.1:p.Ala353Val missense NM_001406991.1:c.1616_1617delinsTT NP_001393920.1:p.Ala539Val missense NM_001406992.1:c.1616_1617delinsTT NP_001393921.1:p.Ala539Val missense NM_001406993.1:c.1058_1059delinsTT NP_001393922.1:p.Ala353Val missense NM_001406994.1:c.992_993delinsTT NP_001393923.1:p.Ala331Val missense NM_001406995.1:c.1058_1059delinsTT NP_001393924.1:p.Ala353Val missense NM_001406996.1:c.1058_1059delinsTT NP_001393925.1:p.Ala353Val missense NM_001406997.1:c.1058_1059delinsTT NP_001393926.1:p.Ala353Val missense NM_001406998.1:c.1280_1281delinsTT NP_001393927.1:p.Ala427Val missense NM_001406999.1:c.992_993delinsTT NP_001393928.1:p.Ala331Val missense NM_001407000.1:c.992_993delinsTT NP_001393929.1:p.Ala331Val missense NM_001407001.1:c.992_993delinsTT NP_001393930.1:p.Ala331Val missense NM_001407002.1:c.1058_1059delinsTT NP_001393931.1:p.Ala353Val missense NM_001407003.1:c.1058_1059delinsTT NP_001393932.1:p.Ala353Val missense NM_170708.4:c.1608+429_1608+430delinsTT intron variant NR_047544.1:n.2257_2258delCCinsTT NR_047545.1:n.1504_1505delCCinsTT NC_000001.11:g.156137661_156137662delinsTT NC_000001.10:g.156107452_156107453delinsTT NG_008692.2:g.60089_60090delinsTT LRG_254:g.60089_60090delinsTT LRG_254t1:c.1616_1617delCCinsTT LRG_254p1:p.Ala539Val LRG_254t2:c.1616_1617delCCinsTT LRG_254p2:p.Ala539Val - Protein change
- A331V, A353V, A427V, A440V, A458V, A539V
- Other names
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- Canonical SPDI
- NC_000001.11:156137660:CC:TT
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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
Help
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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LMNA | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1839 | 2119 |
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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- | RCV004557278.2 |
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
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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
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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
(-)
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criteria provided, single submitter
Method: clinical testing
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Emery-Dreifuss muscular dystrophy 2, autosomal dominant
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP)
Accession: SCV005046458.1
First in ClinVar: Jun 02, 2024 Last updated: Jun 02, 2024 |
Comment:
The variant was detected in a 7-years-old boy with persistent elevation of creatinine kinase, tiptoe gait and remarkable clinical worsening during last year. The main … (more)
The variant was detected in a 7-years-old boy with persistent elevation of creatinine kinase, tiptoe gait and remarkable clinical worsening during last year. The main suspicion was muscular dystrophy or polyneuropathy. The c.1616_1617delCCinsTT variant in the exon 10 of LMNA (NM_170707.4) results in a change of the predicted protein (p.Ala539Val). The variant is not detected in general population. Similar variant LMNA(NM_170707.4):c.1616C>T (p.Ala539Val) has been reported in ClinVar as “uncertain significance”. In silico tools classifies de variant as "patohogenic strong" and being a very unfrequent in population and "de novo" variant, we think is related with the patient observed clinic. (less)
Number of individuals with the variant: 1
Clinical Features:
Tip-toe gait (present) , Elevated circulating creatine kinase concentration (present)
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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 Jun 23, 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.