NM_001113490.2:c.2957C>G

Variant summary

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

The NM_001113490.2(AMOT):ā€‹c.2957C>Gā€‹(p.Pro986Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000893 in 111,929 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000089 ( 0 hom., 1 hem., cov: 23)

Consequence

AMOT
NM_001113490.2 missense

Scores

1
2
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.77
Variant links:
Genes affected
AMOT (HGNC:17810): (angiomotin) This gene belongs to the motin family of angiostatin binding proteins characterized by conserved coiled-coil domains and C-terminal PDZ binding motifs. The encoded protein is expressed predominantly in endothelial cells of capillaries as well as larger vessels of the placenta where it may mediate the inhibitory effect of angiostatin on tube formation and the migration of endothelial cells toward growth factors during the formation of new blood vessels. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

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=0.08943465).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AMOTNM_001113490.2 linkc.2957C>G p.Pro986Arg missense_variant Exon 13 of 14 ENST00000371959.9 NP_001106962.1 Q4VCS5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AMOTENST00000371959.9 linkc.2957C>G p.Pro986Arg missense_variant Exon 13 of 14 1 NM_001113490.2 ENSP00000361027.3 Q4VCS5-1
AMOTENST00000371962.5 linkc.2261C>G p.Pro754Arg missense_variant Exon 10 of 11 1 ENSP00000361030.1 E7ERM3
AMOTENST00000304758.5 linkc.1730C>G p.Pro577Arg missense_variant Exon 11 of 12 1 ENSP00000305557.1 Q4VCS5-2

Frequencies

GnomAD3 genomes
AF:
0.00000894
AC:
1
AN:
111875
Hom.:
0
Cov.:
23
AF XY:
0.0000294
AC XY:
1
AN XY:
34037
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:
0.00
Gnomad NFE
AF:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
12
GnomAD4 genome
AF:
0.00000893
AC:
1
AN:
111929
Hom.:
0
Cov.:
23
AF XY:
0.0000293
AC XY:
1
AN XY:
34101
show subpopulations
Gnomad4 AFR
AF:
0.00
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:
0.0000188
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
21
DANN
Benign
0.87
DEOGEN2
Benign
0.030
T;.;T;T
FATHMM_MKL
Benign
0.35
N
LIST_S2
Benign
0.49
T;T;T;.
M_CAP
Benign
0.0083
T
MetaRNN
Benign
0.089
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L;.;.;L
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-0.13
N;N;N;N
REVEL
Benign
0.010
Sift
Pathogenic
0.0
D;.;D;D
Sift4G
Uncertain
0.045
D;D;D;D
Polyphen
0.065
B;.;.;B
Vest4
0.30
MutPred
0.28
Loss of loop (P = 0.0128);.;.;Loss of loop (P = 0.0128);
MVP
0.34
MPC
0.33
ClinPred
0.25
T
GERP RS
2.0
Varity_R
0.079
gMVP
0.20

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

LitVar

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

Other links and lift over

dbSNP: rs148609725; hg19: chrX-112022425; API