19-15475860-CA-TC

Variant names:

• chr19-15475860-CA-TC
• NM_052890.4:c.809_810delTGinsGA
• PGLYRP2 p.Met270Arg

Variant summary

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

The NM_052890.4(PGLYRP2):​c.809_810delTGinsGA​(p.Met270Arg) 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: PGLYRP2 NM_052890.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 0 publications found

Genes affected

PGLYRP2 (HGNC:30013): (peptidoglycan recognition protein 2) This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. This protein hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in bacterial cell wall glycopeptides, and thus may play a scavenger role by digesting biologically active peptidoglycan into biologically inactive fragments. [provided by RefSeq, Sep 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052890.4. 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
	PGLYRP2	NM_052890.4	MANE Select	c.809_810delTGinsGA	p.Met270Arg	missense	N/A	NP_443122.3
	PGLYRP2	NM_001363546.1		c.809_810delTGinsGA	p.Met270Arg	missense	N/A	NP_001350475.1	Q96PD5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGLYRP2	ENST00000340880.5	TSL:1 MANE Select	c.809_810delTGinsGA	p.Met270Arg	missense	N/A	ENSP00000345968.4	Q96PD5-1
	PGLYRP2	ENST00000292609.8	TSL:1	c.809_810delTGinsGA	p.Met270Arg	missense	N/A	ENSP00000292609.3	Q96PD5-2
	PGLYRP2	ENST00000851095.1		c.809_810delTGinsGA	p.Met270Arg	missense	N/A	ENSP00000521154.1

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		0.096

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: chr19-15586671;