1-33036804-C-A

Variant names:

• chr1-33036804-C-A
• rs267606647
• NM_001625.4:c.25G>T

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001625.4(AK2):​c.25G>T​(p.Glu9*) variant causes a stop gained change involving the alteration of a non-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 Pathogenic (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: AK2 NM_001625.4 stop_gained
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.573
• Publications: 3 publications found

Genes affected

AK2 (HGNC:362): (adenylate kinase 2) Adenylate kinases are involved in regulating the adenine nucleotide composition within a cell by catalyzing the reversible transfer of phosphate groups among adenine nucleotides. Three isozymes of adenylate kinase, namely 1, 2, and 3, have been identified in vertebrates; this gene encodes isozyme 2. Expression of these isozymes is tissue-specific and developmentally regulated. Isozyme 2 is localized in the mitochondrial intermembrane space and may play a role in apoptosis. Mutations in this gene are the cause of reticular dysgenesis. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 1 and 2.[provided by RefSeq, Nov 2010]

AK2 Gene-Disease associations (from GenCC):

• reticular dysgenesis

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, Orphanet, G2P

ENSG00000236065 (HGNC:58388):

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 22 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-33036804-C-A is Pathogenic according to our data. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-33036804-C-A is described in CliVar as Pathogenic. Clinvar id is 18262.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AK2	NM_001625.4	c.25G>T	p.Glu9*	stop_gained	Exon 1 of 6	ENST00000672715.1	NP_001616.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AK2	ENST00000672715.1	c.25G>T	p.Glu9*	stop_gained	Exon 1 of 6		NM_001625.4	ENSP00000499935.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1444164 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 716930

African (AFR) AF: 0.00 AC: 0 AN: 33176

American (AMR) AF: 0.00 AC: 0 AN: 42688

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25750

East Asian (EAS) AF: 0.00 AC: 0 AN: 39002

South Asian (SAS) AF: 0.00 AC: 0 AN: 83680

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51648

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4284

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1104378

Other (OTH) AF: 0.00 AC: 0 AN: 59558

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Reticular dysgenesis Pathogenic:1

Jan 01, 2009

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Uncertain	0.0
CADD	Pathogenic	36
DANN	Uncertain	0.99
Eigen	Benign	0.058
Eigen_PC	Benign	-0.29
FATHMM_MKL	Uncertain	0.80	D
PhyloP100		0.57
Vest4		0.75
GERP RS		0.87
PromoterAI		-0.030	Neutral
Mutation Taster		=1/199	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs267606647; hg19: chr1-33502405;