ClinVar Genomic variation as it relates to human health
NM_001353921.2(ARHGEF9):c.928_935del (p.Ser310fs)
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_001353921.2(ARHGEF9):c.928_935del (p.Ser310fs)
Variation ID: 2501758 Accession: VCV002501758.1
- Type and length
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Deletion, 8 bp
- Location
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Cytogenetic: Xq11.1 X: 63674048-63674055 (GRCh38) [ NCBI UCSC ] X: 62893928-62893935 (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 May 20, 2023 May 20, 2023 Sep 7, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001353921.2:c.928_935del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001340850.1:p.Ser310fs frameshift NM_001173479.2:c.748_755del NP_001166950.1:p.Ser250fs frameshift NM_001173480.2:c.601_608del NP_001166951.1:p.Ser201fs frameshift NM_001330495.2:c.844_851del NP_001317424.1:p.Ser282fs frameshift NM_001353922.2:c.928_935del NP_001340851.1:p.Ser310fs frameshift NM_001353923.1:c.946_953del NP_001340852.1:p.Ser316fs frameshift NM_001353924.2:c.727_734del NP_001340853.1:p.Ser243fs frameshift NM_001353926.2:c.727_734del NP_001340855.1:p.Ser243fs frameshift NM_001353927.2:c.844_851del NP_001340856.1:p.Ser282fs frameshift NM_001353928.2:c.907_914del NP_001340857.1:p.Ser303fs frameshift NM_001369030.1:c.907_914del NP_001355959.1:p.Ser303fs frameshift NM_001369031.1:c.907_914del NP_001355960.1:p.Ser303fs frameshift NM_001369032.1:c.907_914del NP_001355961.1:p.Ser303fs frameshift NM_001369033.1:c.844_851del NP_001355962.1:p.Ser282fs frameshift NM_001369034.1:c.844_851del NP_001355963.1:p.Ser282fs frameshift NM_001369035.1:c.844_851del NP_001355964.1:p.Ser282fs frameshift NM_001369036.1:c.844_851del NP_001355965.1:p.Ser282fs frameshift NM_001369037.1:c.844_851del NP_001355966.1:p.Ser282fs frameshift NM_001369038.1:c.844_851del NP_001355967.1:p.Ser282fs frameshift NM_001369039.1:c.727_734del NP_001355968.1:p.Ser243fs frameshift NM_001369040.1:c.727_734del NP_001355969.1:p.Ser243fs frameshift NM_001369041.1:c.844_851del NP_001355970.1:p.Ser282fs frameshift NM_001369042.1:c.601_608del NP_001355971.1:p.Ser201fs frameshift NM_001369043.1:c.844_851del NP_001355972.1:p.Ser282fs frameshift NM_001369044.1:c.844_851del NP_001355973.1:p.Ser282fs frameshift NM_001369045.1:c.493_500del NP_001355974.1:p.Ser165fs frameshift NM_015185.3:c.907_914del NP_056000.1:p.Ser303fs frameshift NC_000023.11:g.63674050_63674057del NC_000023.10:g.62893930_62893937del NG_016975.1:g.116492_116499del - Protein change
- S165fs, S201fs, S243fs, S250fs, S282fs, S303fs, S310fs, S316fs
- Other names
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- Canonical SPDI
- NC_000023.11:63674047:AGGACAGAAG:AG
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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
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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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ARHGEF9 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
432 | 562 |
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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Pathogenic (1) |
criteria provided, single submitter
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Sep 7, 2022 | RCV003228180.1 |
Submissions - Germline
Classification
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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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Pathogenic
(Sep 07, 2022)
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criteria provided, single submitter
Method: clinical testing
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Developmental and epileptic encephalopathy, 8
Affected status: unknown
Allele origin:
germline
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Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV003924243.1
First in ClinVar: May 20, 2023 Last updated: May 20, 2023 |
Comment:
This variant has not been reported in the literature and is not present in large control databases. Evolutionary conservation and computational predictive tools for this … (more)
This variant has not been reported in the literature and is not present in large control databases. Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is a deletion of 8 nucleotides at amino acid position 303 and creates a premature stop codon 39 amino acids downstream from this location which results in an absent or abnormal protein. Loss of function variants have been reported in association with disease for this gene (Ghesh 2021 PMID:33600053). In summary, data on this variant is highly suspicious for disease, but requires further evidence for pathogenicity. Therefore, this variant is classified as Likely Pathogenic . (less)
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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 Aug 06, 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.