8-58433161-CA-TG

Variant names:

• chr8-58433161-CA-TG
• NM_001077619.2:c.341_342delCAinsTG
• UBXN2B p.Ser114Leu

Variant summary

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

The NM_001077619.2(UBXN2B):​c.341_342delCAinsTG​(p.Ser114Leu) variant causes a missense, splice region change. 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: UBXN2B NM_001077619.2 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.70
• Publications: 0 publications found

Genes affected

UBXN2B (HGNC:27035): (UBX domain protein 2B) Predicted to enable ubiquitin binding activity. Involved in establishment of mitotic spindle orientation; negative regulation of protein localization to centrosome; and positive regulation of mitotic centrosome separation. Predicted to be located in Golgi apparatus; endoplasmic reticulum; and spindle pole centrosome. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077619.2. 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
	UBXN2B	NM_001077619.2	MANE Select	c.341_342delCAinsTG	p.Ser114Leu	missense splice_region	N/A	NP_001071087.1	Q14CS0
	UBXN2B	NM_001363181.1		c.341_342delCAinsTG	p.Ser114Leu	missense splice_region	N/A	NP_001350110.1
	UBXN2B	NM_001330535.2		c.341_342delCAinsTG	p.Ser114Leu	missense splice_region	N/A	NP_001317464.1	E5RJ36

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN2B	ENST00000399598.7	TSL:1 MANE Select	c.341_342delCAinsTG	p.Ser114Leu	missense splice_region	N/A	ENSP00000382507.2	Q14CS0
	UBXN2B	ENST00000970427.1		c.329_330delCAinsTG	p.Ser110Leu	missense splice_region	N/A	ENSP00000640486.1
	UBXN2B	ENST00000879980.1		c.341_342delCAinsTG	p.Ser114Leu	missense splice_region	N/A	ENSP00000550039.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.7

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: chr8-59345720;