NM_001367493.1:c.4343C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001367493.1(ARHGEF4):​c.4343C>T​(p.Ala1448Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000505 in 1,584,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

ARHGEF4
NM_001367493.1 missense

Scores

1
1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.986
Variant links:
Genes affected
ARHGEF4 (HGNC:684): (Rho guanine nucleotide exchange factor 4) Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein coupled receptors. The protein encoded by this gene may form complex with G proteins and stimulate Rho-dependent signals. Multiple alternatively spliced transcript variants encoding different isoforms have been found, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jun 2013]
SMIM39 (HGNC:54076): (small integral membrane protein 39) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09662643).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARHGEF4NM_001367493.1 linkc.4343C>T p.Ala1448Val missense_variant Exon 7 of 14 ENST00000409359.7 NP_001354422.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARHGEF4ENST00000409359.7 linkc.4343C>T p.Ala1448Val missense_variant Exon 7 of 14 5 NM_001367493.1 ENSP00000386794.3 E7EV07

Frequencies

GnomAD3 genomes
AF:
0.0000328
AC:
5
AN:
152242
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000121
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:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000991
AC:
2
AN:
201810
Hom.:
0
AF XY:
0.00000916
AC XY:
1
AN XY:
109226
show subpopulations
Gnomad AFR exome
AF:
0.000172
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000209
AC:
3
AN:
1432108
Hom.:
0
Cov.:
32
AF XY:
0.00000141
AC XY:
1
AN XY:
710144
show subpopulations
Gnomad4 AFR exome
AF:
0.0000307
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000182
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000328
AC:
5
AN:
152242
Hom.:
0
Cov.:
33
AF XY:
0.0000403
AC XY:
3
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.000121
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264
ExAC
AF:
0.0000166
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Apr 01, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.785C>T (p.A262V) alteration is located in exon 7 (coding exon 5) of the ARHGEF4 gene. This alteration results from a C to T substitution at nucleotide position 785, causing the alanine (A) at amino acid position 262 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
11
DANN
Uncertain
0.99
DEOGEN2
Benign
0.018
T;T;.;.;.;.
Eigen
Benign
-0.73
Eigen_PC
Benign
-0.74
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.70
T;T;T;T;T;T
M_CAP
Pathogenic
0.41
D
MetaRNN
Benign
0.097
T;T;T;T;T;T
MetaSVM
Benign
-0.61
T
MutationAssessor
Benign
1.6
.;L;.;L;.;.
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-0.78
.;N;.;N;.;N
REVEL
Benign
0.11
Sift
Benign
0.13
.;T;.;T;.;T
Sift4G
Benign
0.41
.;T;T;T;.;T
Polyphen
0.0060, 0.029
.;B;.;B;.;.
Vest4
0.15, 0.17, 0.16, 0.15
MutPred
0.25
.;Loss of disorder (P = 0.3157);Loss of disorder (P = 0.3157);Loss of disorder (P = 0.3157);.;.;
MVP
0.86
MPC
0.12
ClinPred
0.080
T
GERP RS
4.0
Varity_R
0.11
gMVP
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs748787186; hg19: chr2-131797626; COSMIC: COSV58117750; COSMIC: COSV58117750; API