NM_001337.4:c.565_567delGTGinsCTT

Variant names:

• chr3-39265943-CAC-AAG
• NM_001337.4:c.565_567delGTGinsCTT
• CX3CR1 p.Val189Leu

Variant summary

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

The NM_001337.4(CX3CR1):​c.565_567delGTGinsCTT​(p.Val189Leu) 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. V189M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CX3CR1 NM_001337.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10
• Publications: 0 publications found

Genes affected

CX3CR1 (HGNC:2558): (C-X3-C motif chemokine receptor 1) Fractalkine is a transmembrane protein and chemokine involved in the adhesion and migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. The encoded protein also is a coreceptor for HIV-1, and some variations in this gene lead to increased susceptibility to HIV-1 infection and rapid progression to AIDS. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001337.4. 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
	CX3CR1	NM_001337.4	MANE Select	c.565_567delGTGinsCTT	p.Val189Leu	missense	N/A	NP_001328.1	P49238-1
	CX3CR1	NM_001171174.1		c.661_663delGTGinsCTT	p.Val221Leu	missense	N/A	NP_001164645.1	P49238-4
	CX3CR1	NM_001171171.2		c.565_567delGTGinsCTT	p.Val189Leu	missense	N/A	NP_001164642.1	P49238-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CR1	ENST00000399220.3	TSL:1 MANE Select	c.565_567delGTGinsCTT	p.Val189Leu	missense	N/A	ENSP00000382166.3	P49238-1
	CX3CR1	ENST00000358309.3	TSL:2	c.661_663delGTGinsCTT	p.Val221Leu	missense	N/A	ENSP00000351059.3	P49238-4
	CX3CR1	ENST00000541347.5	TSL:4	c.565_567delGTGinsCTT	p.Val189Leu	missense	N/A	ENSP00000439140.1	P49238-1

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		3.1

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: chr3-39307434;