NM_003559.5:c.258-548_258-530delTGCAGGTTCCCACTGTAGT

Variant names:

• chr17-38784868-TACTACAGTGGGAACCTGCA-T
• NM_003559.5:c.258-548_258-530delTGCAGGTTCCCACTGTAGT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PP5_Moderate

The NM_003559.5(PIP4K2B):​c.258-548_258-530delTGCAGGTTCCCACTGTAGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PIP4K2B NM_003559.5 intron
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.361
• Publications: 0 publications found

Genes affected

PIP4K2B (HGNC:8998): (phosphatidylinositol-5-phosphate 4-kinase type 2 beta) The protein encoded by this gene catalyzes the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. The encoded protein sequence does not show similarity to other kinases, but the protein does exhibit kinase activity. Additionally, the encoded protein interacts with p55 TNF receptor. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PP5: Variant 17-38784868-TACTACAGTGGGAACCTGCA-T is Pathogenic according to our data. Variant chr17-38784868-TACTACAGTGGGAACCTGCA-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 3779551.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003559.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP4K2B	NM_003559.5	MANE Select	c.258-548_258-530delTGCAGGTTCCCACTGTAGT		intron	N/A	NP_003550.1	P78356-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP4K2B	ENST00000619039.5	TSL:1 MANE Select	c.258-548_258-530delTGCAGGTTCCCACTGTAGT		intron	N/A	ENSP00000482548.1	P78356-1
	PIP4K2B	ENST00000862415.1		c.258-548_258-530delTGCAGGTTCCCACTGTAGT		intron	N/A	ENSP00000532474.1
	PIP4K2B	ENST00000617499.1	TSL:4	c.66-548_66-530delTGCAGGTTCCCACTGTAGT		intron	N/A	ENSP00000477549.1	A0A087WT35

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Hereditary neutrophilia;C4310764:Autosomal recessive severe congenital neutropenia due to CSF3R deficiency (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

hg19: chr17-36941121;