chr5-157240122-AT-A
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_005546.4(ITK):c.913delT(p.Tyr305ThrfsTer27) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y305Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
ITK
NM_005546.4 frameshift
NM_005546.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.84
Publications
0 publications found
Genes affected
ITK (HGNC:6171): (IL2 inducible T cell kinase) This gene encodes an intracellular tyrosine kinase expressed in T-cells. The protein contains both SH2 and SH3 domains which are often found in intracellular kinases. It is thought to play a role in T-cell proliferation and differentiation. [provided by RefSeq, Jul 2008]
ITK Gene-Disease associations (from GenCC):
- lymphoproliferative syndromeInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- lymphoproliferative syndrome 1Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-157240122-AT-A is Pathogenic according to our data. Variant chr5-157240122-AT-A is described in CliVar as Pathogenic. Clinvar id is 521210.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-157240122-AT-A is described in CliVar as Pathogenic. Clinvar id is 521210.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-157240122-AT-A is described in CliVar as Pathogenic. Clinvar id is 521210.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-157240122-AT-A is described in CliVar as Pathogenic. Clinvar id is 521210.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-157240122-AT-A is described in CliVar as Pathogenic. Clinvar id is 521210.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Jul 28, 2016
Ambry Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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