rs121434593

chr19-40237979-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2 PP2 PP3_Strong PP5_Moderate

The NM_001626.6(AKT2):c.821G>A(p.Arg274His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R274R) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AKT2 NM_001626.6 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.91

Genes affected

AKT2 (HGNC:392): (AKT serine/threonine kinase 2) This gene is a putative oncogene encoding a protein belonging to a subfamily of serine/threonine kinases containing SH2-like (Src homology 2-like) domains, which is involved in signaling pathways. The gene serves as an oncogene in the tumorigenesis of cancer cells For example, its overexpression contributes to the malignant phenotype of a subset of human ductal pancreatic cancers. The encoded protein is a general protein kinase capable of phophorylating several known proteins, and has also been implicated in insulin signaling. [provided by RefSeq, Nov 2019]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, AKT2
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.982
• PP5: Variant 19-40237979-C-T is Pathogenic according to our data. Variant chr19-40237979-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 13982.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKT2	NM_001626.6	c.821G>A	p.Arg274His	missense_variant	9/14	ENST00000392038.7
AKT2	NM_001330511.1	c.821G>A	p.Arg274His	missense_variant	8/12
AKT2	NM_001243027.3	c.635G>A	p.Arg212His	missense_variant	9/14
AKT2	NM_001243028.3	c.635G>A	p.Arg212His	missense_variant	8/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKT2	ENST00000392038.7	c.821G>A	p.Arg274His	missense_variant	9/14	1	NM_001626.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Type 2 diabetes mellitus Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Feb 01, 2009

- -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

May 25, 2023

Observed in a family with severe insulin resistance and diabetes mellitus (George et al., 2004); Published functional studies demonstrate a damaging effect to protein function in human liver cells and rat fat cells (George et al., 2004; Chan et al., 2011); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22031698, 19164855, 33901270, 35755045, 35250856, 37105912, 33893069, 15166380) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
Cadd	Pathogenic	33
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.62	D;.;.;.;.
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.94	D;D;.;D;D
M_CAP	Benign	0.053	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Uncertain	0.26	D
MutationAssessor	Pathogenic	3.1	M;M;M;.;.
MutationTaster	Benign	1.0	A;A;A
PrimateAI	Pathogenic	0.91	D
PROVEAN	Uncertain	-4.2	D;D;D;.;.
REVEL	Uncertain	0.63
Sift	Pathogenic	0.0	D;D;D;.;.
Sift4G	Uncertain	0.020	D;D;D;D;.
Polyphen		1.0	D;.;.;.;.
Vest4		0.98
MutPred		0.98		Gain of methylation at K277 (P = 0.1057);Gain of methylation at K277 (P = 0.1057);Gain of methylation at K277 (P = 0.1057);.;.;
MVP		0.92
MPC		1.1
ClinPred		1.0	D
GERP RS		4.0
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		2.7
Varity_R		0.89
gMVP		0.98

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

Other links and lift over

dbSNP: rs121434593; hg19: chr19-40743886;