ClinVar Genomic variation as it relates to human health
NM_001395002.1(MAP4K4):c.3458_3459del (p.Val1153fs)
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_001395002.1(MAP4K4):c.3458_3459del (p.Val1153fs)
Variation ID: 1804004 Accession: VCV001804004.1
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 2q11.2 2: 101882623-101882624 (GRCh38) [ NCBI UCSC ] 2: 102499085-102499086 (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 Dec 24, 2022 Dec 24, 2022 May 20, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001395002.1:c.3458_3459del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001381931.1:p.Val1153fs frameshift NM_001242559.2:c.3023_3024del NP_001229488.1:p.Val1008fs frameshift NM_001242560.2:c.3011_3012del NP_001229489.1:p.Val1004fs frameshift NM_001384476.1:c.3101_3102del NP_001371405.1:p.Val1034fs frameshift NM_001384477.1:c.3290_3291del NP_001371406.1:p.Val1097fs frameshift NM_001384478.1:c.2780_2781del NP_001371407.1:p.Val927fs frameshift NM_001384480.1:c.2972_2973delTT NP_001371409.1:p.Val991Glyfs frameshift NM_001384481.1:c.3218_3219del NP_001371410.1:p.Val1073fs frameshift NM_001384482.1:c.2771_2772del NP_001371411.1:p.Val924fs frameshift NM_001384483.1:c.3053_3054del NP_001371412.1:p.Val1018fs frameshift NM_001384484.1:c.3104_3105del NP_001371413.1:p.Val1035fs frameshift NM_001384485.1:c.3104_3105del NP_001371414.1:p.Val1035fs frameshift NM_001384486.1:c.3227_3228del NP_001371415.1:p.Val1076fs frameshift NM_001384487.1:c.3194_3195del NP_001371416.1:p.Val1065fs frameshift NM_001384488.1:c.3224_3225del NP_001371417.1:p.Val1075fs frameshift NM_001384489.1:c.2282_2283delTT NP_001371418.1:p.Val761Glyfs frameshift NM_001384490.1:c.2873_2874del NP_001371419.1:p.Val958fs frameshift NM_001384491.1:c.3008_3009del NP_001371420.1:p.Val1003fs frameshift NM_001384492.1:c.3362_3363del NP_001371421.1:p.Val1121fs frameshift NM_001384493.1:c.3296_3297del NP_001371422.1:p.Val1099fs frameshift NM_001384494.1:c.2870_2871del NP_001371423.1:p.Val957fs frameshift NM_001384495.1:c.2972_2973del NP_001371424.1:p.Val991fs frameshift NM_001384496.1:c.3056_3057del NP_001371425.1:p.Val1019fs frameshift NM_001384497.1:c.3449_3450del NP_001371426.1:p.Val1150fs frameshift NM_001384505.1:c.1742_1743delTT NP_001371434.1:p.Val581Glyfs frameshift NM_001384506.1:c.3266_3267del NP_001371435.1:p.Val1089fs frameshift NM_001384507.1:c.3035_3036del NP_001371436.1:p.Val1012fs frameshift NM_001384508.1:c.3098_3099del NP_001371437.1:p.Val1033fs frameshift NM_001384509.1:c.3191_3192del NP_001371438.1:p.Val1064fs frameshift NM_001384520.1:c.3164_3165del NP_001371449.1:p.Val1055fs frameshift NM_001384543.1:c.3173_3174del NP_001371472.1:p.Val1058fs frameshift NM_001384544.1:c.2381_2382delTT NP_001371473.1:p.Val794Glyfs frameshift NM_001384545.1:c.2189_2190delTT NP_001371474.1:p.Val730Glyfs frameshift NM_001384548.1:c.3209_3210del NP_001371477.1:p.Val1070fs frameshift NM_001384549.1:c.2945_2946del NP_001371478.1:p.Val982fs frameshift NM_001384550.1:c.2990_2991del NP_001371479.1:p.Val997fs frameshift NM_001384551.1:c.2915_2916del NP_001371480.1:p.Val972fs frameshift NM_001384552.1:c.3074_3075del NP_001371481.1:p.Val1025fs frameshift NM_001384553.1:c.3263_3264del NP_001371482.1:p.Val1088fs frameshift NM_001384554.1:c.2975_2976del NP_001371483.1:p.Val992fs frameshift NM_001384555.1:c.3269_3270del NP_001371484.1:p.Val1090fs frameshift NM_001384556.1:c.3068_3069del NP_001371485.1:p.Val1023fs frameshift NM_001384557.1:c.2906_2907del NP_001371486.1:p.Val969fs frameshift NM_001384558.1:c.2984_2985del NP_001371487.1:p.Val995fs frameshift NM_001384559.1:c.2942_2943del NP_001371488.1:p.Val981fs frameshift NM_001384560.1:c.2837_2838del NP_001371489.1:p.Val946fs frameshift NM_001384561.1:c.2753_2754del NP_001371490.1:p.Val918fs frameshift NM_001384562.1:c.3071_3072del NP_001371491.1:p.Val1024fs frameshift NM_001384563.1:c.3260_3261del NP_001371492.1:p.Val1087fs frameshift NM_001384564.1:c.3329_3330del NP_001371493.1:p.Val1110fs frameshift NM_001384567.1:c.3176_3177del NP_001371496.1:p.Val1059fs frameshift NM_001384572.1:c.3077_3078del NP_001371501.1:p.Val1026fs frameshift NM_001384579.1:c.3008_3009del NP_001371508.1:p.Val1003fs frameshift NM_004834.5:c.2777_2778del NP_004825.3:p.Val926fs frameshift NM_145686.4:c.3125_3126del NP_663719.2:p.Val1042fs frameshift NM_145687.4:c.2942_2943del NP_663720.1:p.Val981fs frameshift NR_169279.1:n.3399_3400del non-coding transcript variant NR_169280.1:n.3498_3499del non-coding transcript variant NR_169281.1:n.3306_3307del non-coding transcript variant NR_169282.1:n.2859_2860del non-coding transcript variant NC_000002.12:g.101882623_101882624del NC_000002.11:g.102499085_102499086del - Protein change
- V1003fs, V1004fs, V1008fs, V1012fs, V1018fs, V1019fs, V1023fs, V1024fs, V1025fs, V1026fs, V1033fs, V1034fs, V1035fs, V1042fs, V1055fs, V1058fs, V1059fs, V1064fs, V1065fs, V1070fs, V1073fs, V1075fs, V1076fs, V1087fs, V1088fs, V1089fs, V1090fs, V1097fs, V1099fs, V1110fs, V1121fs, V1150fs, V1153fs, V918fs, V924fs, V926fs, V927fs, V946fs, V957fs, V958fs, V969fs, V972fs, V981fs, V982fs, V991fs, V992fs, V995fs, V997fs
- Other names
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- Canonical SPDI
- NC_000002.12:101882622: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
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
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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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MAP4K4 | - | - |
GRCh38 GRCh37 |
100 | 127 |
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
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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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Likely pathogenic (1) |
criteria provided, single submitter
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May 20, 2022 | RCV002468742.4 |
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
(May 20, 2022)
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criteria provided, single submitter
Method: clinical testing
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Imperforate anus
Renal dysplasia (Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Accession: SCV002764781.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Number of individuals with the variant: 1
Clinical Features:
Imperforate anus (present) , Renal dysplasia (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 May 12, 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.