X-112780975-C-A

Variant names:

• chrX-112780975-C-A
• NM_001113490.2:c.2384G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001113490.2(AMOT):​c.2384G>T​(p.Gly795Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: AMOT NM_001113490.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.08

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMOT	NM_001113490.2	c.2384G>T	p.Gly795Val	missense_variant	Exon 12 of 14	ENST00000371959.9	NP_001106962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMOT	ENST00000371959.9	c.2384G>T	p.Gly795Val	missense_variant	Exon 12 of 14	1	NM_001113490.2	ENSP00000361027.3
AMOT	ENST00000371962.5	c.1688G>T	p.Gly563Val	missense_variant	Exon 9 of 11	1		ENSP00000361030.1
AMOT	ENST00000304758.5	c.1157G>T	p.Gly386Val	missense_variant	Exon 10 of 12	1		ENSP00000305557.1
AMOT	ENST00000371958.1	c.1688G>T	p.Gly563Val	missense_variant	Exon 9 of 9	5		ENSP00000361026.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Sep 24, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2384G>T (p.G795V) alteration is located in exon 9 (coding exon 9) of the AMOT gene. This alteration results from a G to T substitution at nucleotide position 2384, causing the glycine (G) at amino acid position 795 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	0.16
BayesDel_addAF	Benign	-0.019	T
BayesDel_noAF	Benign	-0.27
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.14	T;.;T;T;T
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.84	T;T;T;.;T
M_CAP	Pathogenic	0.60	D
MetaRNN	Uncertain	0.61	D;D;D;D;D
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.0	M;.;.;M;.
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-2.3	N;N;N;N;D
REVEL	Benign	0.12
Sift	Uncertain	0.020	D;.;D;D;D
Sift4G	Benign	0.084	T;T;T;T;T
Polyphen		0.95	P;.;.;P;.
Vest4		0.67
MutPred		0.20		Loss of catalytic residue at A794 (P = 0.0625);.;.;Loss of catalytic residue at A794 (P = 0.0625);.;
MVP		0.42
MPC		0.38
ClinPred		0.91	D
GERP RS		5.7
Varity_R		0.58
gMVP		0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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-112024203;