rs782139620
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS1_Supporting
The NM_001353921.2(ARHGEF9):c.667C>T(p.Arg223Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000914 in 1,203,270 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R223H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001353921.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF9 | NM_001353921.2 | c.667C>T | p.Arg223Cys | missense_variant | 5/10 | ENST00000671741.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF9 | ENST00000671741.2 | c.667C>T | p.Arg223Cys | missense_variant | 5/10 | NM_001353921.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000898 AC: 1AN: 111343Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33553
GnomAD3 exomes AF: 0.0000416 AC: 7AN: 168404Hom.: 0 AF XY: 0.0000181 AC XY: 1AN XY: 55198
GnomAD4 exome AF: 0.00000916 AC: 10AN: 1091927Hom.: 0 Cov.: 30 AF XY: 0.00000279 AC XY: 1AN XY: 358279
GnomAD4 genome ? AF: 0.00000898 AC: 1AN: 111343Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33553
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 04, 2022 | Variant summary: ARHGEF9 c.646C>T (p.Arg216Cys) results in a non-conservative amino acid change located in the Dbl homology (DH) domain (IPR000219) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.2e-05 in 168404 control chromosomes (gnomAD), including one hemizgyote. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.646C>T has been reported in the literature in one hemizygotic individual affected with isolated Developmental Disorder (Dong_2020), however this report does not provide unequivocal conclusions about association of the variant with Early Infantile Epileptic Encephalopathy 8. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One ClinVar submitter has assessed the variant since 2014: the variant was classified as of uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 02, 2021 | - - |
Developmental and epileptic encephalopathy, 8 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 216 of the ARHGEF9 protein (p.Arg216Cys). This variant is present in population databases (rs782139620, gnomAD 0.02%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with clinical features of ARHGEF9-related conditions (PMID: 32005694). ClinVar contains an entry for this variant (Variation ID: 571820). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ARHGEF9 protein function. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at