17-43661283-CTG-TTC

Variant names:

• chr17-43661283-CTG-TTC
• NM_004527.4:c.250_252delCAGinsGAA
• MEOX1 p.Gln84Glu

Variant summary

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

The NM_004527.4(MEOX1):​c.250_252delCAGinsGAA​(p.Gln84Glu) 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: 31)
• Consequence: MEOX1 NM_004527.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.88
• Publications: 0 publications found

Genes affected

MEOX1 (HGNC:7013): (mesenchyme homeobox 1) This gene encodes a member of a subfamily of non-clustered, diverged, antennapedia-like homeobox-containing genes. The encoded protein may play a role in the molecular signaling network regulating somite development. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

MEOX1 Gene-Disease associations (from GenCC):

• Klippel-Feil syndrome 2, autosomal recessive

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• isolated Klippel-Feil syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004527.4. 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
	MEOX1	NM_004527.4	MANE Select	c.250_252delCAGinsGAA	p.Gln84Glu	missense	N/A	NP_004518.1	P50221-1
	MEOX1	NM_013999.4		c.250_252delCAGinsGAA	p.Gln84Glu	missense	N/A	NP_054705.1	P50221-2
	MEOX1	NM_001040002.2		c.-96_-94delCAGinsGAA		5_prime_UTR	Exon 2 of 4	NP_001035091.1	P50221-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX1	ENST00000318579.9	TSL:1 MANE Select	c.250_252delCAGinsGAA	p.Gln84Glu	missense	N/A	ENSP00000321684.4	P50221-1
	MEOX1	ENST00000549132.2	TSL:1	c.250_252delCAGinsGAA	p.Gln84Glu	missense	N/A	ENSP00000449049.2	P50221-2
	MEOX1	ENST00000909611.1		c.250_252delCAGinsGAA	p.Gln84Glu	missense	N/A	ENSP00000579670.1

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		4.9

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: chr17-41738651;