X-101657244-GGC-AGA

Variant names:

• chrX-101657244-GGC-AGA
• NM_177949.4:c.343_345delGCCinsTCT
• ARMCX2 p.Ala115Ser

Variant summary

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

The NM_177949.4(ARMCX2):​c.343_345delGCCinsTCT​(p.Ala115Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 24)
• Consequence: ARMCX2 NM_177949.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 0 publications found

Genes affected

ARMCX2 (HGNC:16869): (armadillo repeat containing X-linked 2) This gene encodes a protein containing a potential N-terminal transmembrane domain and multiple armadillo (arm) repeats. Proteins containing arm repeats are involved in development, maintenance of tissue integrity, and tumorigenesis. This gene is located in a cluster of related genes on chromosome X. There is a pseudogene for this gene on chromosome 7. Alternative splicing in the 5' UTR results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2013]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_177949.4. 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
	ARMCX2	NM_177949.4	MANE Select	c.343_345delGCCinsTCT	p.Ala115Ser	missense	N/A	NP_808818.1	Q7L311
	ARMCX2	NM_001282231.2		c.343_345delGCCinsTCT	p.Ala115Ser	missense	N/A	NP_001269160.1	Q7L311
	ARMCX2	NM_014782.7		c.343_345delGCCinsTCT	p.Ala115Ser	missense	N/A	NP_055597.1	Q7L311

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX2	ENST00000356824.9	TSL:1 MANE Select	c.343_345delGCCinsTCT	p.Ala115Ser	missense	N/A	ENSP00000349281.4	Q7L311
	ARMCX2	ENST00000328766.9	TSL:1	c.343_345delGCCinsTCT	p.Ala115Ser	missense	N/A	ENSP00000331662.5	Q7L311
	ARMCX2	ENST00000330154.6	TSL:1	c.343_345delGCCinsTCT	p.Ala115Ser	missense	N/A	ENSP00000328631.2	Q7L311

Frequencies

GnomAD3 genomes Cov.: 24

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

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.2

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: chrX-100912230;