6-150065984-TC-CA

Variant names:

• chr6-150065984-TC-CA
• NM_024518.3:c.266_267delGAinsTG
• ULBP3 p.Gly89Val

Variant summary

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

The NM_024518.3(ULBP3):​c.266_267delGAinsTG​(p.Gly89Val) variant causes a missense 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 MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G89E) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ULBP3 NM_024518.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 0 publications found

Genes affected

ULBP3 (HGNC:14895): (UL16 binding protein 3) The protein encoded by this gene is one of several related ligands of the KLRK1/NKG2D receptor, which is found in primary NK cells. Binding of these ligands to the receptor activates several signal transduction pathways, including the JAK2, STAT5, and ERK pathways. The encoded protein is expressed solubly and on the surface of many tumor cells, making it potentially an important target for therapeutics. [provided by RefSeq, Nov 2015]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024518.3. 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
	ULBP3	NM_024518.3	MANE Select	c.266_267delGAinsTG	p.Gly89Val	missense	N/A	NP_078794.1	Q9BZM4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ULBP3	ENST00000367339.7	TSL:5 MANE Select	c.266_267delGAinsTG	p.Gly89Val	missense	N/A	ENSP00000356308.1	Q9BZM4
	ULBP3	ENST00000438272.2	TSL:1	c.266_267delGAinsTG	p.Gly89Val	missense	N/A	ENSP00000403562.2	Q9BZM4
	ULBP3	ENST00000925509.1		c.119_120delGAinsTG	p.Gly40Val	missense	N/A	ENSP00000595568.1

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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-150387120;