4-153703544-CTG-TTA

Variant names:

• chr4-153703544-CTG-TTA
• NM_001318789.2:c.637_639delCTGinsTTA
• TLR2 p.214

Variant summary

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

The NM_001318789.2(TLR2):​c.637_639delCTGinsTTA​(p.214) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. L213L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TLR2 NM_001318789.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.21
• Publications: 0 publications found

Genes affected

TLR2 (HGNC:11848): (toll like receptor 2) The protein encoded by this gene is a member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. This protein is a cell-surface protein that can form heterodimers with other TLR family members to recognize conserved molecules derived from microorganisms known as pathogen-associated molecular patterns (PAMPs). Activation of TLRs by PAMPs leads to an up-regulation of signaling pathways to modulate the host's inflammatory response. This gene is also thought to promote apoptosis in response to bacterial lipoproteins. This gene has been implicated in the pathogenesis of several autoimmune diseases. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318789.2. 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
	TLR2	NM_001318789.2	MANE Select	c.637_639delCTGinsTTA	p.214	synonymous	N/A	NP_001305718.1	O60603
	TLR2	NM_001318787.2		c.637_639delCTGinsTTA	p.214	synonymous	N/A	NP_001305716.1	A0A0S2Z4S4
	TLR2	NM_001318790.2		c.637_639delCTGinsTTA	p.214	synonymous	N/A	NP_001305719.1	A0A0S2Z4S4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR2	ENST00000642700.2	MANE Select	c.637_639delCTGinsTTA	p.214	synonymous	N/A	ENSP00000494425.1	O60603
	TLR2	ENST00000260010.7	TSL:6	c.637_639delCTGinsTTA	p.214	synonymous	N/A	ENSP00000260010.6	O60603
	TLR2	ENST00000642580.1		c.637_639delCTGinsTTA	p.214	synonymous	N/A	ENSP00000495339.1	O60603

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		5.2

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: chr4-154624696;