Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 37126546)
ClinVar Genomic variation as it relates to human health
NM_001395002.1(MAP4K4):c.52del (p.Leu18fs)
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)
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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 pathogenic
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_001395002.1(MAP4K4):c.52del (p.Leu18fs)
Variation ID: 3340992 Accession: VCV003340992.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2q11.2 2: 101698130 (GRCh38) [ NCBI UCSC ] 2: 102314592 (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 Oct 8, 2024 Oct 8, 2024 Aug 1, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001395002.1:c.52del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001381931.1:p.Leu18fs frameshift NM_001242559.2:c.52del NP_001229488.1:p.Leu18fs frameshift NM_001242560.2:c.52del NP_001229489.1:p.Leu18fs frameshift NM_001384476.1:c.52del NP_001371405.1:p.Leu18fs frameshift NM_001384477.1:c.52del NP_001371406.1:p.Leu18fs frameshift NM_001384478.1:c.52del NP_001371407.1:p.Leu18fs frameshift NM_001384481.1:c.52del NP_001371410.1:p.Leu18fs frameshift NM_001384482.1:c.52del NP_001371411.1:p.Leu18fs frameshift NM_001384483.1:c.52del NP_001371412.1:p.Leu18fs frameshift NM_001384484.1:c.52del NP_001371413.1:p.Leu18fs frameshift NM_001384485.1:c.52del NP_001371414.1:p.Leu18fs frameshift NM_001384486.1:c.52del NP_001371415.1:p.Leu18fs frameshift NM_001384487.1:c.52del NP_001371416.1:p.Leu18fs frameshift NM_001384488.1:c.52del NP_001371417.1:p.Leu18fs frameshift NM_001384490.1:c.52del NP_001371419.1:p.Leu18fs frameshift NM_001384491.1:c.52del NP_001371420.1:p.Leu18fs frameshift NM_001384492.1:c.52del NP_001371421.1:p.Leu18fs frameshift NM_001384493.1:c.52del NP_001371422.1:p.Leu18fs frameshift NM_001384494.1:c.52del NP_001371423.1:p.Leu18fs frameshift NM_001384495.1:c.52del NP_001371424.1:p.Leu18fs frameshift NM_001384496.1:c.52del NP_001371425.1:p.Leu18fs frameshift NM_001384497.1:c.52del NP_001371426.1:p.Leu18fs frameshift NM_001384506.1:c.52del NP_001371435.1:p.Leu18fs frameshift NM_001384507.1:c.52del NP_001371436.1:p.Leu18fs frameshift NM_001384508.1:c.52del NP_001371437.1:p.Leu18fs frameshift NM_001384509.1:c.52del NP_001371438.1:p.Leu18fs frameshift NM_001384520.1:c.52del NP_001371449.1:p.Leu18fs frameshift NM_001384543.1:c.52del NP_001371472.1:p.Leu18fs frameshift NM_001384548.1:c.52del NP_001371477.1:p.Leu18fs frameshift NM_004834.5:c.52del NP_004825.3:p.Leu18fs frameshift NM_145686.4:c.52del NP_663719.2:p.Leu18fs frameshift NM_145687.4:c.52del NP_663720.1:p.Leu18fs frameshift NR_169279.1:n.426del non-coding transcript variant NR_169280.1:n.426del non-coding transcript variant NR_169281.1:n.426del non-coding transcript variant NR_169282.1:n.426del non-coding transcript variant NC_000002.12:g.101698132del NC_000002.11:g.102314594del - Protein change
- L18fs
- Other names
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- Canonical SPDI
- NC_000002.12:101698129:CCC:CC
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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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| MAP4K4 | - | - |
GRCh38 GRCh37 |
133 | 160 | |
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 pathogenic (1) |
criteria provided, single submitter
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Aug 1, 2023 | RCV004722274.1 |
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 pathogenic
(Aug 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV005326898.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function … (more)
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 37126546) (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:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 37126546)
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 Oct 08, 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.