17-43848692-CGC-GGT

Variant names:

• chr17-43848692-CGC-GGT
• NM_145273.4:c.178_180delCGCinsGGT
• CD300LG p.Arg60Gly

Variant summary

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

The NM_145273.4(CD300LG):​c.178_180delCGCinsGGT​(p.Arg60Gly) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R60H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD300LG NM_145273.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 0 publications found

Genes affected

CD300LG (HGNC:30455): (CD300 molecule like family member g) Members of the CD300 (see MIM 606786)-like (CD300L) family, such as CD300LG, are widely expressed on hematopoietic cells. All CD300L proteins are type I cell surface glycoproteins that contain a single immunoglobulin (Ig) V-like domain (Takatsu et al., 2006 [PubMed 16876123]).[supplied by OMIM, Mar 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145273.4. 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
	CD300LG	NM_145273.4	MANE Select	c.178_180delCGCinsGGT	p.Arg60Gly	missense	N/A	NP_660316.2	Q6UXG3-1
	CD300LG	NM_001168322.2		c.178_180delCGCinsGGT	p.Arg60Gly	missense	N/A	NP_001161794.1	Q6UXG3-4
	CD300LG	NM_001168323.2		c.178_180delCGCinsGGT	p.Arg60Gly	missense	N/A	NP_001161795.1	Q6UXG3-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD300LG	ENST00000317310.5	TSL:1 MANE Select	c.178_180delCGCinsGGT	p.Arg60Gly	missense	N/A	ENSP00000321005.3	Q6UXG3-1
	CD300LG	ENST00000539718.5	TSL:1	c.178_180delCGCinsGGT	p.Arg60Gly	missense	N/A	ENSP00000442368.1	Q6UXG3-4
	CD300LG	ENST00000293396.12	TSL:1	c.178_180delCGCinsGGT	p.Arg60Gly	missense	N/A	ENSP00000293396.7	Q6UXG3-2

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		1.3

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: chr17-41926060;