11-17330136-CAG-GAA

Variant names:

• chr11-17330136-CAG-GAA
• NM_005013.4:c.1012_1014delCAGinsGAA
• NUCB2 p.Gln338Glu

Variant summary

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

The NM_005013.4(NUCB2):​c.1012_1014delCAGinsGAA​(p.Gln338Glu) variant causes a missense 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NUCB2 NM_005013.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.79
• Publications: 0 publications found

Genes affected

NUCB2 (HGNC:8044): (nucleobindin 2) This gene encodes a protein with a suggested role in calcium level maintenance, eating regulation in the hypothalamus, and release of tumor necrosis factor from vascular endothelial cells. This protein binds calcium and has EF-folding domains. [provided by RefSeq, Oct 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005013.4. 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
	NUCB2	NM_005013.4	MANE Select	c.1012_1014delCAGinsGAA	p.Gln338Glu	missense	N/A	NP_005004.1	P80303-1
	NUCB2	NM_001352661.2		c.1015_1017delCAGinsGAA	p.Gln339Glu	missense	N/A	NP_001339590.1
	NUCB2	NM_001352663.2		c.1015_1017delCAGinsGAA	p.Gln339Glu	missense	N/A	NP_001339592.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUCB2	ENST00000529010.6	TSL:1 MANE Select	c.1012_1014delCAGinsGAA	p.Gln338Glu	missense	N/A	ENSP00000436455.1	P80303-1
	NUCB2	ENST00000646648.1		n.*324_*326delCAGinsGAA		non_coding_transcript_exon	Exon 14 of 17	ENSP00000495210.1	A0A2R8Y6G7
	NUCB2	ENST00000646648.1		n.*324_*326delCAGinsGAA		3_prime_UTR	Exon 14 of 17	ENSP00000495210.1	A0A2R8Y6G7

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		6.8

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: chr11-17351683;