Variant rs756693906 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3

The NM_004098.4(EMX2):c.167_178delCCGCCGCCGCCG(p.Ala56_Ala59del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)

Consequence

EMX2
NM_004098.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.70

Variant links:

Genes affected

EMX2 (HGNC:3341): (empty spiracles homeobox 2) This gene encodes a homeobox-containing transcription factor that is the homolog to the 'empty spiracles' gene in Drosophila. Research on this gene in humans has focused on its expression in three tissues: dorsal telencephalon, olfactory neuroepithelium, and urogenetial system. It is expressed in the dorsal telencephalon during development in a low rostral-lateral to high caudal-medial gradient and is proposed to pattern the neocortex into defined functional areas. It is also expressed in embryonic and adult olfactory neuroepithelia where it complexes with eukaryotic translation initiation factor 4E (eIF4E) and possibly regulates mRNA transport or translation. In the developing urogenital system, it is expressed in epithelial tissues and is negatively regulated by HOXA10. Alternative splicing results in multiple transcript variants encoding distinct proteins.[provided by RefSeq, Sep 2009]

EMX2 links:

EMX2OS (HGNC:):

EMX2OS links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP3

Nonframeshift variant in repetitive region in NM_004098.4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMX2	NM_004098.4 linkuse as main transcript	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	1/3	ENST00000553456.5	NP_004089.1	Q04743-1
EMX2	NM_001165924.2 linkuse as main transcript	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	1/2		NP_001159396.1	Q04743-2
EMX2OS	NR_002791.2 linkuse as main transcript	n.574+868_574+879delGGCGGCGGCGGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
EMX2	ENST00000553456.5 linkuse as main transcript	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	1/3	1	NM_004098.4	ENSP00000450962.3	Q04743-1
EMX2OS	ENST00000551288.5 linkuse as main transcript	n.574+868_574+879delGGCGGCGGCGGC		intron_variant		1
EMX2	ENST00000442245.5 linkuse as main transcript	c.167_178delCCGCCGCCGCCG	p.Ala56_Ala59del	disruptive_inframe_deletion	1/2	2		ENSP00000474874.1	Q04743-2

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.