9-5073770-G-T

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 11P and 1B. PM5PP3PP5_Very_StrongBS1_Supporting

The NM_004972.4(JAK2):c.1849G>T(p.Val617Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000293 in 1,605,918 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V617I) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.00036 ( 1 hom., cov: 33)

Exomes 𝑓: 0.00029 ( 16 hom. )

Consequence

JAK2
NM_004972.4 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:24O:2

Conservation

PhyloP100: 9.55

Variant links:

Genes affected

JAK2 (HGNC:6192): (Janus kinase 2) This gene encodes a non-receptor tyrosine kinase that plays a central role in cytokine and growth factor signalling. The primary isoform of this protein has an N-terminal FERM domain that is required for erythropoietin receptor association, an SH2 domain that binds STAT transcription factors, a pseudokinase domain and a C-terminal tyrosine kinase domain. Cytokine binding induces autophosphorylation and activation of this kinase. This kinase then recruits and phosphorylates signal transducer and activator of transcription (STAT) proteins. Growth factors like TGF-beta 1 also induce phosphorylation and activation of this kinase and translocation of downstream STAT proteins to the nucleus where they influence gene transcription. Mutations in this gene are associated with numerous inflammatory diseases and malignancies. This gene is a downstream target of the pleiotropic cytokine IL6 that is produced by B cells, T cells, dendritic cells and macrophages to produce an immune response or inflammation. Disregulation of the IL6/JAK2/STAT3 signalling pathways produces increased cellular proliferation and myeloproliferative neoplasms of hematopoietic stem cells. A nonsynonymous mutation in the pseudokinase domain of this gene disrupts the domains inhibitory effect and results in constitutive tyrosine phosphorylation activity and hypersensitivity to cytokine signalling. This gene and the IL6/JAK2/STAT3 signalling pathway is a therapeutic target for the treatment of excessive inflammatory responses to viral infections. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2020]

JAK2 links:

INSL6 (HGNC:6089): (insulin like 6) The protein encoded by this gene contains a classical signature of the insulin superfamily and is significantly similar to relaxin and relaxin-like factor. This gene is preferentially expressed in testis. Its expression in testis is restricted to interstitial cells surrounding seminiferous tubules, which suggests a role in sperm development and fertilization. [provided by RefSeq, Jul 2008]

INSL6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PM5

Other missense variant is known to change same aminoacid residue: Variant chr9-5073770-G-A is described in Lovd as [Pathogenic].

PP3

MetaRNN computational evidence supports a deleterious effect, 0.809

PP5

Variant 9-5073770-G-T is Pathogenic according to our data. Variant chr9-5073770-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 14662.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-5073770-G-T is described in Lovd as [Pathogenic].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000362 (55/151910) while in subpopulation SAS AF= 0.000622 (3/4824). AF 95% confidence interval is 0.000317. There are 1 homozygotes in gnomad4. There are 26 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAK2	NM_004972.4 link	c.1849G>T	p.Val617Phe	missense_variant	Exon 14 of 25	ENST00000381652.4	NP_004963.1	O60674

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAK2	ENST00000381652.4 link	c.1849G>T	p.Val617Phe	missense_variant	Exon 14 of 25	1	NM_004972.4	ENSP00000371067.4		O60674
JAK2	ENST00000636127.1 link	c.1849G>T	p.Val617Phe	missense_variant	Exon 14 of 16	5		ENSP00000489812.1		A0A1B0GTR9

Frequencies

GnomAD3 genomes

AF:

0.000362

AC:

AN:

151910

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000363

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000866

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.000284

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000442

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000352

AC:

AN:

250262

Hom.:

AF XY:

0.000333

AC XY:

AN XY:

135324

show subpopulations

Gnomad AFR exome

AF:

0.000309

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.000597

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.000328

Gnomad FIN exome

AF:

0.000561

Gnomad NFE exome

AF:

0.000397

Gnomad OTH exome

AF:

0.000164

GnomAD4 exome

AF:

0.000286

AC:

416

AN:

1454008

Hom.:

Cov.:

AF XY:

0.000343

AC XY:

248

AN XY:

723690

show subpopulations

Gnomad4 AFR exome

AF:

0.000120

Gnomad4 AMR exome

AF:

0.000157

Gnomad4 ASJ exome

AF:

0.000730

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.000279

Gnomad4 FIN exome

AF:

0.000302

Gnomad4 NFE exome

AF:

0.000295

Gnomad4 OTH exome

AF:

0.000216

GnomAD4 genome

AF:

0.000362

AC:

AN:

151910

Hom.:

Cov.:

AF XY:

0.000350

AC XY:

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.000363

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000866

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.000284

Gnomad4 NFE

AF:

0.000442

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000492

Hom.:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.000692

AC:

EpiCase

AF:

0.0000546

EpiControl

AF:

0.000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:24Other:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Acquired polycythemia vera

Pathogenic:6

Jan 01, 2022

Provincial Medical Genetics Program of British Columbia, University of British Columbia

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 02, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Molecular Diagnostics Laboratory, University of Rochester Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: provider interpretation

- -

Feb 08, 2018

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1849G>T (p.V617F) variant in the JAK2 gene is commonly reported as a somatic change in myeloproliferative neoplasms (MPNs) including polycythemia vera, essential thrombocythemia, primary myelofibrosis [PMID: 15781101, 15858187, 15837627, 19074595]. Recently, this variant has also been described as one of the most common drivers of age-related clonal hematopoiesis [PMID: 27563148]. The c.1849G>T (p.V617F) variant in the JAK2 gene is classified as a pathogenic somatic variant. -

Feb 15, 2024

3billion

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is observed at an allele frequency greater than expected for the associated disorder in the gnomAD v2.1.1 dataset and therefore considered benign. Predicted Consequence/Location: Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.88 (>=0.6, sensitivity 0.68 and specificity 0.92)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000014662). A different missense change at the same codon (p.Val617Ile) has been reported to be associated with JAK2 related disorder (ClinVar ID: VCV000029763 /PMID: 22397670). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline. -

Aug 07, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided

Pathogenic:6

Nov 29, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces valine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 617 of the JAK2 protein (p.Val617Phe). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant is a well-known somatic change that has been reported as a recurrent variant in many individuals affected with myeloproliferative disorders (PMID: 15920007, 15781101, 15858187, 15793561, 16603627). ClinVar contains an entry for this variant (Variation ID: 14662). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt JAK2 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects JAK2 function (PMID: 15793561, 23535062). A different missense substitution at this codon (p.Val617Ile) has been reported to segregate with autosomal dominant hereditary thrombocytosis as a germline change in a single family (PMID: 22397670). Functional studies show that this variant results in constitutive kinase activation and cytokine hyper-responsiveness (PMID: 23535062, 22397670). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

JAK2: PM1, PM5, PM6, PS4:Moderate, PP4, PS3:Supporting -

Sep 06, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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: 23425079, 25698270, 21120162, 21689158, 27777768, 28205126, 24381227, 16755940, 16293597, 29349042, 31721094, 28596259, 29641446, 23300178, 16156870, 16871278, 20182460, 24068492, 15781101, 19287384, 25157968, 24986690, 16081687, 16709929, 18394554, 24404189, 20339092, 22571758, 20631743, 23115274, 22818858, 22041374, 22829971, 22422826, 21160067, 19549988, 16341032, 26228487, 23537216, 23248577, 23057517, 19195039, 17596137, 17440677, 17194663, 16990759, 16904848, 16954506, 16926301, 15920007, 15858187, 15860661, 26556299, 19293426, 16762626, 15793561, 30944118, 33144682, 32581362, 31447099, 19327411, 27389715, 35861108, 37885353, 35150601) -

Feb 26, 2024

Centre for Clinical Genetics and Genomic Diagnostics, Zealand University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary myelofibrosis

Pathogenic:3

Aug 07, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Aug 30, 2021

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 24, 2022

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

_x000D_ Criteria applied: PS3, PS4, PM1, PM5, PP4 -

Thrombocythemia 3

Pathogenic:2

Oct 03, 2022

Revvity Omics, Revvity

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 07, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Primary myelofibrosis;C0023467:Acute myeloid leukemia;C0032463:Acquired polycythemia vera;C0856761:Budd-Chiari syndrome;C3281125:Thrombocythemia 3;C4551637:Primary familial polycythemia due to EPO receptor mutation

Pathogenic:2

Oct 31, 2018

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting+PS3+PS4+PM6_Supporting -

JAK2-related disorder

Pathogenic:1

Apr 30, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The JAK2 c.1849G>T variant is predicted to result in the amino acid substitution p.Val617Phe. This variant has been reported to be present in almost all patients with polycythemia vera and more than half of those with essential thrombocytosis and primary myelofibrosis (Vassiliou 2016. PubMed ID: 27563148). Somatic c.1849G>T variants have been reported in myeloproliferative neoplasms (Ortmann et al. 2015. PubMed ID: 25671252; Rumi et al. 2014. PubMed ID: 24986690). This variant is reported in 0.058% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. This variant is interpreted as pathogenic. -

Myeloproliferative disorder

Pathogenic:1

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Polycythemia

Pathogenic:1

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Primary myelofibrosis;C0038002:Splenomegaly

Pathogenic:1

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Acute myeloid leukemia

Pathogenic:1

Aug 07, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Primary familial polycythemia due to EPO receptor mutation

Other:1

Aug 07, 2014

OMIM

Significance: Affects

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Budd-Chiari syndrome, susceptibility to, somatic

Other:1

Aug 07, 2014

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Pathogenic

0.20

BayesDel_noAF

Pathogenic

0.36

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.85

.;D

Eigen

Pathogenic

0.85

Eigen_PC

Pathogenic

0.84

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.77

T;T

M_CAP

Pathogenic

0.34

MetaRNN

Pathogenic

0.81

D;D

MetaSVM

Uncertain

0.44

MutationAssessor

Uncertain

2.1

.;M

PrimateAI

Uncertain

0.70

PROVEAN

Uncertain

-3.9

.;D

REVEL

Pathogenic

0.88

Sift

Uncertain

0.0020

.;D

Sift4G

Uncertain

0.0070

.;D

Polyphen

1.0

.;D

Vest4

0.89

MVP

0.97

MPC

0.84

ClinPred

0.92

GERP RS

5.5

Varity_R

0.88

gMVP

0.72

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over