NM_004098.4:c.238A>G

Variant names:

• chr10-117543505-A-G
• rs770506828
• NM_004098.4:c.238A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_004098.4(EMX2):​c.238A>G​(p.Asn80Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000881 in 1,135,570 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N80K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 8.8e-7 (0 hom.)
• Consequence: EMX2 NM_004098.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.80
• Publications: 2 publications found

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]

EMX2OS (HGNC:18511): (EMX2 opposite strand/antisense RNA)

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004098.4. 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
	EMX2	NM_004098.4	MANE Select	c.238A>G	p.Asn80Asp	missense	Exon 1 of 3	NP_004089.1	Q04743-1
	EMX2	NM_001165924.2		c.238A>G	p.Asn80Asp	missense	Exon 1 of 2	NP_001159396.1	Q04743-2
	EMX2OS	NR_002791.2		n.574+801T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2	ENST00000553456.5	TSL:1 MANE Select	c.238A>G	p.Asn80Asp	missense	Exon 1 of 3	ENSP00000450962.3	Q04743-1
	EMX2OS	ENST00000551288.5	TSL:1	n.574+801T>C		intron	N/A
	EMX2	ENST00000442245.5	TSL:2	c.238A>G	p.Asn80Asp	missense	Exon 1 of 2	ENSP00000474874.1	Q04743-2

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 8.81e-7 AC: 1 AN: 1135570 Hom.: 0 Cov.: 34 AF XY: 0.00000177 AC XY: 1 AN XY: 563800

African (AFR) AF: 0.00 AC: 0 AN: 25610

American (AMR) AF: 0.00 AC: 0 AN: 36264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18350

East Asian (EAS) AF: 0.00 AC: 0 AN: 23400

South Asian (SAS) AF: 0.00 AC: 0 AN: 74482

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33290

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4424

European-Non Finnish (NFE) AF: 0.00000114 AC: 1 AN: 876240

Other (OTH) AF: 0.00 AC: 0 AN: 43510

GnomAD4 genome Cov.: 27

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Uncertain	25
DANN	Benign	0.45
DEOGEN2	Benign	0.34	T
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.21
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.88	D
M_CAP	Pathogenic	0.96	D
MetaRNN	Uncertain	0.48	T
MetaSVM	Uncertain	-0.27	T
MutationAssessor	Benign	0.0	N
PhyloP100		4.8
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-1.8	N
REVEL	Uncertain	0.38
Sift	Benign	0.41	T
Sift4G	Benign	0.62	T
Polyphen		0.12	B
Vest4		0.51
MutPred		0.23		Gain of phosphorylation at S76 (P = 0.166)
MVP		0.91
ClinPred		0.92	D
GERP RS		4.8
PromoterAI		-0.012	Neutral
Varity_R		0.30
gMVP		0.71
Mutation Taster		=78/22	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs770506828; hg19: chr10-119303016;