X-63638103-A-C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6

The NM_001353921.2(ARHGEF9):​c.1497T>G​(p.Phe499Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. F499F) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 22)

Consequence

ARHGEF9
NM_001353921.2 missense

Scores

2
4
11

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: 2.22
Variant links:
Genes affected
ARHGEF9 (HGNC:14561): (Cdc42 guanine nucleotide exchange factor 9) The protein encoded by this gene is a Rho-like GTPase that switches between the active (GTP-bound) state and inactive (GDP-bound) state to regulate CDC42 and other genes. This brain-specific protein also acts as an adaptor protein for the recruitment of gephyrin and together these proteins facilitate receceptor recruitement in GABAnergic and glycinergic synapses. Defects in this gene are the cause of startle disease with epilepsy (STHEE), also known as hyperekplexia with epilepsy, as well as several other types of cognitive disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25487772).
BP6
Variant X-63638103-A-C is Benign according to our data. Variant chrX-63638103-A-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1301616.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARHGEF9NM_001353921.2 linkuse as main transcriptc.1497T>G p.Phe499Leu missense_variant 10/10 ENST00000671741.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARHGEF9ENST00000671741.2 linkuse as main transcriptc.1497T>G p.Phe499Leu missense_variant 10/10 NM_001353921.2 A1

Frequencies

GnomAD3 genomes
AF:
0.00000898
AC:
1
AN:
111344
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
33526
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00420
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 8 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 30, 2022In 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 C15"). ClinVar contains an entry for this variant (Variation ID: 1301616). This missense change has been observed in individual(s) with epileptic encephalopathy with cerebellar atrophy (PMID: 31054490). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 492 of the ARHGEF9 protein (p.Phe492Leu). -
Likely benign, criteria provided, single submitterclinical testingAl Jalila Children’s Genomics Center, Al Jalila Childrens Speciality HospitalFeb 03, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.65
BayesDel_addAF
Benign
-0.014
T
BayesDel_noAF
Benign
-0.26
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.49
T;.;T;T;T;T;T;T;.;T;.;T;T;.;T;.;T
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.78
T;T;T;.;T;.;.;.;T;.;T;.;.;T;.;T;T
M_CAP
Benign
0.019
T
MetaRNN
Benign
0.25
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D
PrimateAI
Pathogenic
0.80
D
PROVEAN
Benign
-2.3
N;.;.;.;.;.;.;.;.;.;.;.;.;.;N;.;.
REVEL
Uncertain
0.36
Sift
Benign
0.36
T;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.
Sift4G
Benign
0.42
T;T;.;.;.;.;.;.;T;T;.;.;.;.;T;T;.
Polyphen
0.0060
B;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
0.33
MutPred
0.38
Loss of phosphorylation at T495 (P = 0.1504);Loss of phosphorylation at T495 (P = 0.1504);.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.92
MPC
1.2
ClinPred
0.45
T
GERP RS
1.6
Varity_R
0.31
gMVP
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-62857983; API