VCV000566826.8 - ClinVar

NM_001353921.2(ARHGEF9):c.442A>G (p.Ser148Gly)

Germline

Classification

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.

(2)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001353921.2(ARHGEF9):c.442A>G (p.Ser148Gly)

Variation ID: 566826 Accession: VCV000566826.8

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xq11.1 X: 63697265 (GRCh38) [ NCBI UCSC ] X: 62917145 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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 10, 2018	Feb 14, 2024	Oct 31, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_001353921.2:c.442A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001340850.1:p.Ser148Gly	missense
NM_001173479.2:c.262A>G	NP_001166950.1:p.Ser88Gly	missense
NM_001173480.2:c.115A>G	NP_001166951.1:p.Ser39Gly	missense
NM_001330495.2:c.358A>G	NP_001317424.1:p.Ser120Gly	missense
NM_001353922.2:c.442A>G	NP_001340851.1:p.Ser148Gly	missense
NM_001353923.1:c.460A>G	NP_001340852.1:p.Ser154Gly	missense
NM_001353924.2:c.241A>G	NP_001340853.1:p.Ser81Gly	missense
NM_001353926.2:c.241A>G	NP_001340855.1:p.Ser81Gly	missense
NM_001353927.2:c.358A>G	NP_001340856.1:p.Ser120Gly	missense
NM_001353928.2:c.421A>G	NP_001340857.1:p.Ser141Gly	missense
NM_001369030.1:c.421A>G	NP_001355959.1:p.Ser141Gly	missense
NM_001369031.1:c.421A>G	NP_001355960.1:p.Ser141Gly	missense
NM_001369032.1:c.421A>G	NP_001355961.1:p.Ser141Gly	missense
NM_001369033.1:c.358A>G	NP_001355962.1:p.Ser120Gly	missense
NM_001369034.1:c.358A>G	NP_001355963.1:p.Ser120Gly	missense
NM_001369035.1:c.358A>G	NP_001355964.1:p.Ser120Gly	missense
NM_001369036.1:c.358A>G	NP_001355965.1:p.Ser120Gly	missense
NM_001369037.1:c.358A>G	NP_001355966.1:p.Ser120Gly	missense
NM_001369038.1:c.358A>G	NP_001355967.1:p.Ser120Gly	missense
NM_001369039.1:c.241A>G	NP_001355968.1:p.Ser81Gly	missense
NM_001369040.1:c.241A>G	NP_001355969.1:p.Ser81Gly	missense
NM_001369041.1:c.358A>G	NP_001355970.1:p.Ser120Gly	missense
NM_001369042.1:c.115A>G	NP_001355971.1:p.Ser39Gly	missense
NM_001369043.1:c.358A>G	NP_001355972.1:p.Ser120Gly	missense
NM_001369044.1:c.358A>G	NP_001355973.1:p.Ser120Gly	missense
NM_001369045.1:c.7A>G	NP_001355974.1:p.Ser3Gly	missense
NM_015185.3:c.421A>G	NP_056000.1:p.Ser141Gly	missense
NC_000023.11:g.63697265T>C
NC_000023.10:g.62917145T>C
NG_016975.1:g.93282A>G

... more HGVS ... less HGVS

Protein change

S141G, S148G, S120G, S39G, S3G, S81G, S88G, S154G

Other names

Canonical SPDI

NC_000023.11:63697264:T:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.00001

Trans-Omics for Precision Medicine (TOPMed) 0.00001

Links

dbSNP: rs1394345886 VarSome

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
Gene	OMIM	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.
ARHGEF9		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	445	578

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.
Developmental and epileptic encephalopathy, 8	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	Oct 31, 2018	RCV000686743.9

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.
Uncertain significance (Oct 31, 2018)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Developmental and epileptic encephalopathy, 8 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV000897578.1 First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019	Publications: PubMed (1) PubMed: 25741868 pmc: 4544753 pmc: 4544753 DOI: 10.1038/gim.2015.30 DOI: 10.1038/gim.2015.30
Uncertain significance (May 29, 2018)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Developmental and epileptic encephalopathy, 8 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000814275.4 First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024	Publications: PubMed (1) PubMed: 28492532 Comment: In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more) In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with ARHGEF9-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with glycine at codon 141 of the ARHGEF9 protein (p.Ser141Gly). The serine residue is highly conserved and there is a small physicochemical difference between serine and glycine. (less)

Comment:

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with ARHGEF9-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with glycine at codon 141 of the ARHGEF9 protein (p.Ser141Gly). The serine residue is highly conserved and there is a small physicochemical difference between serine and glycine.

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:

Citations for germline classification of this variant

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 rs1394345886 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001353921.2(ARHGEF9):c.442A>G (p.Ser148Gly)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1394345886 ...